Parameters

Default parameter values used in simulations.

Alri

Name	Description	Type	Value
base_inc_rate_ALRI_by_RSV	baseline incidence rate of Alri caused by RSV in age groups 0-11, 12-23, 24-59 months, per child per year	List	[0.165623001012122, 0.0368943809605977, 0.011883807410198]
base_inc_rate_ALRI_by_Rhinovirus	baseline incidence of Alri caused by Rhinovirus in age groups 0-11, 12-23, 24-59 months, per child per year	List	[0.0243368081563306, 0.0564272209432261, 0.0181754025659935]
base_inc_rate_ALRI_by_HMPV	baseline incidence of Alri caused by HMPV in age groups 0-11, 12-23, 24-59 months, per child per year	List	[0.0316242920447732, 0.01106932885584, 0.00356546901880363]
base_inc_rate_ALRI_by_Parainfluenza	baseline incidence of Alri caused by Parainfluenza 1-4 in age groups 0-11, 12-23, 24-59 months, per child per year	List	[0.0400689053941642, 0.0125990679490263, 0.00405820325903094]
base_inc_rate_ALRI_by_Strep_pneumoniae_PCV13	baseline incidence of Alri caused by Streptoccocus pneumoniae PCV13 serotype in age groups 0-11, 12-23, 24-59 months, per child per year	List	[0.00839805492638728, 0.0086009815601405, 0.00277040583791159]
base_inc_rate_ALRI_by_Strep_pneumoniae_non_PCV13	baseline incidence of Alri caused by Streptoccocus pneumoniae non PCV13 serotype in age groups 0-11, 12-23, 24-59 months, per child per year	List	[0.00971808948465436, 0.0056295094957977, 0.00181328443302487]
base_inc_rate_ALRI_by_Hib	baseline incidence of Alri caused by Haemophilus influenzae type b in age groups 0-11, 12-23, 24-59 months, per child per year	List	[0.00456369209787862, 0.00223809928508262, 0.000720899502209533]
base_inc_rate_ALRI_by_H.influenzae_non_type_b	baseline incidence of Alri caused by Haemophilus influenzae non-type b in age groups 0-11, 12-23, 24-59 months, per child per year	List	[0.0178046628079453, 0.00771804577106646, 0.00248600917371134]
base_inc_rate_ALRI_by_Enterobacteriaceae	baseline incidence of Alri caused by Enterobacteriaceae in age groups 0-11, 12-23, 24-59 months, per child per year	List	[0.00577447898013911, 0.00776959582619209, 0.002502613624339]
base_inc_rate_ALRI_by_other_Strepto_Enterococci	baseline incidence of Alri caused by other streptococci and Enterococci including Streptococcus pyogenes and Enterococcus faecium in age groups 0-11, 12-23, 24-59 months, per child per year	List	[0.00739221008020393, 0.000441075977443103, 0.000142072094251877]
base_inc_rate_ALRI_by_Staph_aureus	baseline incidence of Alri caused by Staphylococcus aureus in age groups 0-11, 12-23, 24-59 months, per child per year	List	[0.0230583713892271, 0.00164959730828988, 0.000531340984878809]
base_inc_rate_ALRI_by_Influenza	baseline incidence of Alri caused by Influenza type A, B, and C in age groups 0-11, 12-23, 24-59 months, per child per year	List	[0.0156895896609387, 0.00577122651203705, 0.00185893197294524]
base_inc_rate_ALRI_by_P.jirovecii	baseline incidence of Alri caused by P. jirovecii in age groups 0-11, 12-23, 24-59 months, per child per year	List	[0.00532021183938121, 0.00406616141018573, 0.00130972462037058]
base_inc_rate_ALRI_by_other_viral_pathogens	baseline incidence of Alri caused by other viral pathogens in age groups 0-11, 12-23, 24-59 months, per child per year	List	[0.0289052989892286, 0.0340001707821008, 0.0109515723253317]
base_inc_rate_ALRI_by_other_bacterial_pathogens	baseline incidence of Alri caused by other viral pathogens in age groups 0-11, 12-23, 24-59 months, per child per year	List	[0.0340967151177136, 0.0275272316777052, 0.00886661630515269]
base_inc_rate_ALRI_by_other_pathogens_NoS	baseline incidence of Alri caused by other pathogens not otherwise specified in age groups 0-11, 12-23, 24-59 months, per child per year	List	[0.012096954443426, 0.0244908799021158, 0.00788859692140824]
proportion_pneumonia_in_RSV_ALRI	proportion of RSV-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results)	List	[0.469523118748083, 0.493147834326293]
proportion_pneumonia_in_Rhinovirus_ALRI	proportion of Rhinovirus-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results)	List	[0.233411098940226, 0.300943850285401]
proportion_pneumonia_in_HMPV_ALRI	proportion of HMPV-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results)	List	[0.514096212711081, 0.607661832402657]
proportion_pneumonia_in_Parainfluenza_ALRI	proportion of Parainfluenza-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results)	List	[0.381306534835401, 0.586394378700289]
proportion_pneumonia_in_Strep_pneumoniae_PCV13_ALRI	proportion of S. pneumoniae PCV13-type-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results)	List	[0.419837201436785, 1]
proportion_pneumonia_in_Strep_pneumoniae_non_PCV13_ALRI	proportion of S. pneumoniae non PCV13-type-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results)	List	[0.584526531211357, 0.47010416567094]
proportion_pneumonia_in_Hib_ALRI	proportion of Hib ALRI-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results)	List	[0.643816417750475, 0.591228432603006]
proportion_pneumonia_in_H.influenzae_non_type_b_ALRI	proportion of H.influenzae non type-b-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results)	List	[0.484067635967411, 0.685783925920651]
proportion_pneumonia_in_Staph_aureus_ALRI	proportion of S. aureus-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results)	List	[0.314311461687961, 0.668460076932899]
proportion_pneumonia_in_Enterobacteriaceae_ALRI	proportion of Enterobacteriaceae-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results)	List	[0.542743088827561, 0.397386416381317]
proportion_pneumonia_in_other_Strepto_Enterococci_ALRI	proportion of other Streptococci- and Enterococci-attributed ALRI manifesting as pneumoniaby age, (based on PERCH CXR+ results)	List	[0.794939501527616, 1]
proportion_pneumonia_in_Influenza_ALRI	proportion of Influenza-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results)	List	[0.274661773216931, 0.477667070122735]
proportion_pneumonia_in_P.jirovecii_ALRI	proportion of P. jirovecii-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results)	List	[0.773174448993322, 0.650848699225084]
proportion_pneumonia_in_other_viral_pathogens_ALRI	proportion of other viral pathogens-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results)	List	[0.264286065267648, 0.301616616612727]
proportion_pneumonia_in_other_bacterial_pathogens_ALRI	proportion of other bacterial pathogens-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results)	List	[0.321708555070697, 0.424616377668989]
proportion_pneumonia_in_other_pathogens_NoS_ALRI	proportion of other pathogens NoS-attributed ALRI manifesting as pneumonia by age, (based on PERCH CXR+ results)	List	[0.323847892119005, 0.256639724815326]
rr_ALRI_HIV/AIDS	relative rate of acquiring Alri for children with HIV+/AIDS	Real	6.51
rr_ALRI_incomplete_measles_immunisation	relative rate of acquiring Alri for children with incomplete measles immunisation	Real	1.8
rr_ALRI_low_birth_weight	relative rate of acquiring Alri for infants with low birth weight	Real	3.6
rr_ALRI_non_exclusive_breastfeeding	relative rate of acquiring Alri for not exclusive breastfeeding upto 6 months	Real	2.7
rr_ALRI_indoor_air_pollution	relative rate of acquiring Alri for indoor air pollution	Real	1.57
prob_viral_pneumonia_bacterial_coinfection	probability of primary viral pneumonia having a bacterial co-infection	Real	0.3
proportion_bacterial_coinfection_pathogen	list of proportions of each bacterial pathogens in a viral/bacterial co-infection pneumonia,the current values used are the pathogen attributable fractions (AFs) from PERCH for all ages. The AFs were scaled to bacterial pathogens only causes - value assumed to be the proportions of bacterial pathogens causing co-/secondary infection	List	[0.107, 0.072, 0.038, 0.141, 0.134, 0.117, 0.052, 0.338]
max_alri_duration_in_days_without_treatment	maximum duration in days of untreated ALRI episode, assuming an average of 7 days	Real	14.0
overall_progression_to_severe_ALRI	probability of progression to severe ALRI	Real	0.12
prob_pulmonary_complications_in_pneumonia	probability of pulmonary complications in (CXR+) pneumonia	Real	0.215
prob_pleural_effusion_in_pulmonary_complicated_pneumonia	probability of pleural effusion in pneumonia with pulmonary complications	Real	0.938
prob_empyema_in_pulmonary_complicated_pneumonia	probability of empyema in pneumonia with pulmonary complications	Real	0.315
prob_lung_abscess_in_pulmonary_complicated_pneumonia	probability of lung abscess in pneumonia with pulmonary complications	Real	0.049
prob_pneumothorax_in_pulmonary_complicated_pneumonia	probability of pneumothorax in pneumonia with pulmonary complications	Real	0.049
prob_hypoxaemia_in_pneumonia	probability of hypoxaemia in pneumonia cases	Real	0.479
prob_hypoxaemia_in_other_alri	probability of hypoxaemia in bronchiolitis and other alri cases	Real	0.273
prob_bacteraemia_in_pneumonia	probability of bacteraemia in pneumonia	Real	0.039
prob_progression_to_sepsis_with_bacteraemia	probability of progression to sepsis from bactereamia	Real	0.3
proportion_hypoxaemia_with_SpO2<90%	proportion of hypoxaemic children with SpO2 <90%	Real	0.3576
scaler_on_risk_of_death	Multiplicative scaler on the overall risk of death, for the purpose of calibration.	Real	0.75
base_odds_death_ALRI_age<2mo	baseline odds of death from ALRI for young infants aged 0 month and severe pneumonia (base group)	Real	0.041965
or_death_ALRI_age<2mo_very_severe_pneumonia	odds ratio of death from ALRI for young infants with very severe pneumonia	Real	3.994783
or_death_ALRI_age<2mo_P.jirovecii	odds ratio of death from ALRI for young infants with P. jirovecii infection	Real	5.460986
or_death_ALRI_age<2mo_by_month_increase_in_age	odds ratio of death from ALRI for young infants by 1 month increase in age (1 month olds)	Real	0.6033254
base_odds_death_ALRI_age2_59mo	baseline odds of death from ALRI for children aged 2 months, male, no SAM, and non-severe pneumonia classification (base group)	Real	0.0244725
or_death_ALRI_age2_59mo_female	odds ratio of death from ALRI for children who are female	Real	1.327285
or_death_ALRI_age2_59mo_very_severe_pneumonia	odds ratio of death from ALRI for children with very severe pneumonia	Real	8.382832
or_death_ALRI_age2_59mo_P.jirovecii	odds ratio of death from ALRI for children with P. jirovecii infection	Real	13.74696
or_death_ALRI_age2_59mo_by_month_increase_in_age	odds ratio of death from ALRI by 1 month increase in age for 2 to 59 months olds	Real	0.9661072
or_death_ALRI_age2_59mo_SAM	odds ratio of death from ALRI for children with severe acute malnutrition	Real	7.216448
or_death_ALRI_SpO2<90%	odds ratio of death from ALRI for children with oxygen saturation < 90%, base group: SpO2 <=93%	Real	5.04
or_death_ALRI_SpO2_90_92%	odds ratio of death from ALRI for children with oxygen saturation between 09 to 92%, base group: SpO2 <=93%	Real	1.54
or_death_ALRI_sepsis	odds ratio of death from ALRI for children with complication of sepsis (compared to if not)	Real	151.9
or_death_ALRI_pneumothorax	odds ratio of death from ALRI for children with complication of pneumothorax (compared to if not)	Real	77.4
prob_cough_in_pneumonia	probability of cough in pneumonia	Real	1.0
prob_difficult_breathing_in_pneumonia	probability of difficulty breathing in pneumonia	Real	1.0
prob_fever_in_pneumonia	probability of fever in pneumonia	Real	0.82
prob_chest_indrawing_in_pneumonia	probability of chest indrawing in pneumonia	Real	0.74
prob_tachypnoea_in_pneumonia	probability of tachypnoea in pneumonia	Real	0.834
prob_danger_signs_in_pneumonia	probability of any danger sign in pneumonia, including: : unable to drink, convulsions, cyanosis, head nodding/bobbing, irritability, abnormally sleepy, lethargy, nasal flaring, grunting	Real	0.28
prob_cough_in_other_alri	probability of cough in bronchiolitis or other alri	Real	1.0
prob_difficult_breathing_in_other_alri	probability of difficulty breathing in bronchiolitis or other alri	Real	1.0
prob_fever_in_other_alri	probability of fever in bronchiolitis or other alri	Real	0.76
prob_tachypnoea_in_other_alri	probability of tachypnoea in bronchiolitis or other alri	Real	0.758
prob_chest_indrawing_in_other_alri	probability of chest wall indrawing in bronchiolitis or other alri	Real	0.33
prob_danger_signs_in_other_alri	probability of any danger signs in bronchiolitis or other alri	Real	0.3
prob_danger_signs_in_sepsis	probability of any danger signs in ALRI complicated by sepsis	Real	1.0
prob_danger_signs_in_SpO2<90%	probability of any danger signs in children with SpO2 <90%	Real	0.313
prob_danger_signs_in_SpO2_90-92%	probability of any danger signs in children with SpO2 between 90-92%	Real	0.133
prob_chest_indrawing_in_SpO2<90%	probability of chest indrawing in children with SpO2 <90%	Real	0.701
prob_chest_indrawing_in_SpO2_90-92%	probability of chest indrawing in children with SpO2 between 90-92%	Real	0.445
prob_cyanosis_in_other_alri	probability of cyanosis in bronchiolitis or other alri	Real	0.04
prob_cyanosis_in_pneumonia	probability of cyanosis in pneumonia	Real	0.06
prob_cyanosis_in_SpO2<90%	probability of cyanosis when SpO2 < 90%	Real	0.078
rr_Strep_pneum_VT_ALRI_with_PCV13_age<2y	relative rate of acquiring S. pneumoniae vaccine-type Alri for children under 2 years of age immunised wth PCV13	Real	0.18
rr_Strep_pneum_VT_ALRI_with_PCV13_age2to5y	relative rate of acquiring S. pneumoniae vaccine-type Alri for children aged 2 to 5 immunised wth PCV13	Real	0.32
rr_all_strains_Strep_pneum_ALRI_with_PCV13	relative rate of acquiring S. pneumoniae all types Alri for children immunised wth PCV13	Real	0.45
effectiveness_Hib_vaccine_on_Hib_strains	effectiveness of Hib vaccine against H. influenzae typ-b ALRI	Real	0.86
rr_Hib_ALRI_with_Hib_vaccine	relative rate of acquiring H. influenzae type-b Alri for children immunised wth Hib vaccine	Real	0.14
days_between_treatment_and_cure	number of days between any treatment being given in an HSI and the cure occurring.	Integer	28
tf_1st_line_antibiotic_for_severe_pneumonia	Risk of treatment failure for a person with danger_signs_pneumonia being treated with first lineintravenous antibiotics	Real	0.11
rr_tf_1st_line_antibiotics_if_cyanosis	Relative Risk for treatment failure for persons with danger_signs_pneumonia being treated with first line intravenous antibiotics if the person has the symptom of cyanosis.having that symptom.	Real	1.55
rr_tf_1st_line_antibiotics_if_SpO2<90%	Relative Risk for treatment failure for persons with danger_signs_pneumonia being treated with first line intravenous antibiotics if the person has oxygen saturation < 90%.	Real	1.28
rr_tf_1st_line_antibiotics_if_abnormal_CXR	Relative Risk for treatment failure for persons with danger_signs_pneumonia being treated with first line intravenous antibiotics if the person has a disease_type of “pneumonia”.	Real	1.71
rr_tf_1st_line_antibiotics_if_MAM	Relative Risk for treatment failure for persons with danger_signs_pneumonia being treated with first line intravenous antibiotics if the person has un_clinical_acute_malnutrition == “MAM”.	Real	1.48
rr_tf_1st_line_antibiotics_if_SAM	Relative Risk for treatment failure for persons with danger_signs_pneumonia being treated with first line intravenous antibiotics if the person has un_clinical_acute_malnutrition == “SAM”.	Real	2.02
rr_tf_1st_line_antibiotics_if_HIV/AIDS	Relative Risk for treatment failure for persons with danger_signs_pneumonia being treated with first line intravenous antibiotics if the person has HIV and is not currently being treated.	Real	1.8
or_mortality_improved_oxygen_systems	Odds Ratio for the effect of oxygen provision to a person that needs oxygen who receives it, compares to a patient who does not. N.B. The inverse of this is used to reflect the increase in odds of death for a patient that needs oxygen but does not receive it.	Real	0.52
tf_3day_amoxicillin_for_fast_breathing_with_SpO2>=90%	probability of treatment failure by day 6 or relapse by day 14 of 3-day course amoxicillin for treating fast-breathing pneumonia	Real	0.101
tf_3day_amoxicillin_for_chest_indrawing_with_SpO2>=90%	probability of treatment failure by day 6 or relapse by day 14 of 3-day course amoxicillin for treating chest-indrawing pneumonia without hypoxaemia (SpO2>=90%)	Real	0.125
tf_5day_amoxicillin_for_chest_indrawing_with_SpO2>=90%	probability of treatment failure by day 6 or relapse by day 14 of 5-day course amoxicillin for treating chest-indrawing pneumonia without hypoxaemia (SpO2>=90%)	Real	0.108
tf_7day_amoxicillin_for_fast_breathing_pneumonia_in_young_infants	probability of treatment failure by day 6 or relapse by day 14 of 5-day course amoxicillin for treating chest-indrawing pneumonia without hypoxaemia (SpO2>=90%)	Real	0.054
tf_oral_amoxicillin_only_for_severe_pneumonia_with_SpO2>=90%	probability of treatment failure by day 2 for oral amoxicillin given to severe pneumonia (danger-signs) without hypoxaemia (SpO2>=93%)	Real	0.6
tf_oral_amoxicillin_only_for_non_severe_pneumonia_with_SpO2<90%	probability of treatment failure or relapsefor oral amoxicillin given to non-severe pneumonia (fast-breathing or chest-indrawing) with hypoxaemia (SpO2<90%)	Real	0.2826
tf_oral_amoxicillin_only_for_severe_pneumonia_with_SpO2<90%	probability of treatment failure or relapsefor oral amoxicillin given to severe pneumonia (danger-signs) with hypoxaemia (SpO2<90%)	Real	0.8
tf_2nd_line_antibiotic_for_severe_pneumonia	probability of treatment failure by end of IV therapy for 2nd line antibiotic either cloxacillin or ceftriaxone to treat severe pneumonia (danger-signs)	Real	0.235
sensitivity_of_classification_of_fast_breathing_pneumonia_facility_level0	sensitivity of correct classification and treatment decision by the HSA trained in iCCM, using paper-based tools, for fast-breathing pneumonia	Real	0.7
sensitivity_of_classification_of_danger_signs_pneumonia_facility_level0	sensitivity of correct classification and referral decision by the HSA trained in iCCM, using paper-based tools, for danger-signs pneumonia	Real	0.7
sensitivity_of_classification_of_non_severe_pneumonia_facility_level1	sensitivity of correct classification and treatment decision for non-severe pneumonia at facility level 1a and 1b	Real	0.7
sensitivity_of_classification_of_severe_pneumonia_facility_level1	sensitivity of correct classification and referral decision for severe pneumonia at facility level 1a and 1b	Real	0.7
sensitivity_of_classification_of_non_severe_pneumonia_facility_level2	sensitivity of correct classification and treatment decision for non-severe pneumonia at facility level 2	Real	0.7
sensitivity_of_classification_of_severe_pneumonia_facility_level2	sensitivity of correct classification and treatment decision for severe pneumonia at facility level 2	Real	0.7
prob_iCCM_severe_pneumonia_treated_as_fast_breathing_pneumonia	probability of misdiagnosis of iCCM severe pneumonia (with chest-indrawing or danger signs) given treatment for non-severe pneumonia (fast-breathing) at facility level O	Real	0.7
prob_IMCI_severe_pneumonia_treated_as_non_severe_pneumonia	probability of misdiagnosis of IMCI severe pneumonia (with danger signs) given treatment for non-severe pneumonia ( fast-breathing or chest-indrawing) at facility level 1a/1b/2	Real	0.7
or_care_seeking_perceived_severe_illness	The Odds Ratio for healthcare seeking for the symptom of chest-indrawing	Real	2.4
pulse_oximeter_and_oxygen_is_available	Control the availability of the pulse oximeter and oxygen. “Default” does not over-ride availability; “Yes” forces them to be available; “No” forces them to not be available	Categorical	Default
prob_for_followup_if_treatment_failure	The probability for scheduling a follow-up appointment following treatment failure	Real	0.3

BladderCancer

Name	Description	Type	Value
init_prop_bladder_cancer_stage	initial proportions in bladder cancer categories for person aged 15-19 and no tobacco and no schisto_h	List	[5e-05, 5e-05, 5e-05]
init_prop_blood_urine_bladder_cancer_by_stage	initial proportions of those with bladder cancer categories that have the symptom blood urine	List	[0.2, 0.5, 0.7]
init_prop_pelvic_pain_bladder_cancer_by_stage	initial proportions of those with bladder cancer categories that have pelvic pain	List	[0.0, 0.3, 0.5]
init_prop_with_blood_urine_diagnosed_bladder_cancer_by_stage	initial proportions of people that have symptom of blood urine that have been diagnosed	List	[0.7, 0.9, 0.9]
init_prop_with_pelvic_pain_diagnosed_bladder_cancer_by_stage	initial proportions of people that have symptom of pelvic pain that have been diagnosed	List	[0.0, 0.7, 0.9]
init_prop_treatment_status_bladder_cancer	initial proportions of people with bladder cancer that had initiated treatment	List	[0.05, 0.05, 0.05]
init_prob_palliative_care	initial probability of being under palliative care if in metastatic	Real	0.95
r_tis_t1_bladder_cancer_none	probability per 3 months of incident tis_t1 bladder cancer, amongst people with no bladder cancer(for person aged 15-19 and no tobacco and no schisto_h)	Real	1e-05
rr_tis_t1_bladder_cancer_none_age3049	rate ratio for tis_t1 bladder cancer for age 30-49	Real	2.0
rr_tis_t1_bladder_cancer_none_age5069	rate ratio for tis_t1 bladder cancer for age 50-69	Real	3.0
rr_tis_t1_bladder_cancer_none_agege70	rate ratio for tis_t1 bladder cancer for age 70+	Real	3.0
rr_tis_t1_bladder_cancer_none_tobacco	rate ratio for tis_t1 bladder cancer for tobacco smokers	Real	3.5
rr_tis_t1_bladder_cancer_none_schisto_h	rate ratio for tis_t1 bladder cancer for schisto_h	Real	5.0
r_t2p_bladder_cancer_tis_t1	probability per 3 months of t2+ bladder cancer, amongst people with tis_t1 bladder cancer	Real	0.05
rr_t2p_bladder_cancer_undergone_curative_treatment	rate ratio for t2+ bladder cancer for people with tis_t1 bladder cancer if had curative treatment at tis_t1 bladder cancer stage	Real	0.1
r_metastatic_t2p_bladder_cancer	probability per 3 months of metastatic bladder cancer amongst people with t2+ bladder cancer	Real	0.05
rr_metastatic_undergone_curative_treatment	rate ratio for metastatic bladder cancer for people with t2+ bladder cancer if had curative treatment at t2+ bladder cancer stage	Real	0.2
rate_palliative_care_metastatic	prob palliative care this 3 month period if metastatic bladder cancer	Real	0.2
r_death_bladder_cancer	probability per 3 months of death from bladder cancer amongst people with metastatic bladder cancer	Real	0.05
r_blood_urine_tis_t1_bladder_cancer	probability per 3 months of blood_urine in a person with tis_t1 bladder cancer	Real	0.01
rr_blood_urine_t2p_bladder_cancer	rate ratio for blood_urine if have t2p bladder cancer	Real	3.0
rr_blood_urine_metastatic_bladder_cancer	rate ratio for blood_urine if have metastatic bladder cancer	Real	3.0
r_pelvic_pain_tis_t1_bladder_cancer	probability per 3 months of pelvic_pain in a person with tis_t1 bladder cancer	Real	0.0003
rr_pelvic_pain_t2p_bladder_cancer	rate ratio for pelvic_pain if have t2p bladder cancer	Real	200.0
rr_pelvic_pain_metastatic_bladder_cancer	rate ratio for pelvic_pain if have metastatic bladder cancer	Real	300.0
rp_bladder_cancer_age3049	relative prevalence at baseline of bladder cancer/cancer age 30-49	Real	2.0
rp_bladder_cancer_age5069	relative prevalence at baseline of bladder cancer/cancer age 50-69	Real	3.0
rp_bladder_cancer_agege70	relative prevalence at baseline of bladder cancer/cancer age 70+	Real	3.0
rp_bladder_cancer_tobacco	relative prevalence at baseline of bladder cancer if tobacco	Real	3.5
rp_bladder_cancer_schisto_h	relative prevalence at baseline of bladder cancer if schisto_h	Real	5.0
sensitivity_of_cystoscopy_for_bladder_cancer_blood_urine	sensitivity of cystoscopy_for diagnosis of bladder cancer given blood urine	Real	1.0
sensitivity_of_cystoscopy_for_bladder_cancer_pelvic_pain	sensitivity of cystoscopy_for diagnosis of bladder cancer given pelvic pain	Real	1.0

BreastCancer

Name	Description	Type	Value
init_prop_breast_cancer_stage	initial proportions in cancer categories for woman aged 15-29	List	[5e-05, 5e-05, 5e-05, 1.5e-05]
init_prop_breast_lump_discernible_breast_cancer_by_stage	initial proportions of those with cancer categories that have the symptom breast_lump_discernible	List	[0.5, 0.8, 0.9, 0.98]
init_prop_with_breast_lump_discernible_diagnosed_breast_cancer_by_stage	initial proportions of people that have breast_lump_discernible that have been diagnosed	List	[0.9, 0.9, 0.9, 0.9]
init_prop_treatment_status_breast_cancer	initial proportions of people with breast cancer previously treated	List	[0.1, 0.1, 0.1, 0.1]
init_prob_palliative_care	initial probability of being under palliative care if in stage 4	Real	0.8
r_stage1_none	probabilty per 3 months of incident stage 1 breast, amongst people with no breast cancer	Real	2e-06
rr_stage1_none_age3049	rate ratio for stage1 breast cancer for age 30-49	Real	20.0
rr_stage1_none_agege50	rate ratio for stage1 breast cancer for age 50+	Real	20.0
r_stage2_stage1	probabilty per 3 months of stage 2 breast cancer amongst people with stage 1	Real	0.15
rr_stage2_undergone_curative_treatment	rate ratio for stage 2 breast cancer for people with stage 1 breast cancer if had curative treatment at stage 1	Real	0.05
r_stage3_stage2	probabilty per 3 months of stage 3 breast cancer amongst people with stage 2	Real	0.15
rr_stage3_undergone_curative_treatment	rate ratio for stage 3 breast cancer for people with stage 2 breast cancer if had curative treatment at stage 2	Real	0.05
r_stage4_stage3	probabilty per 3 months of stage 4 breast cancer amongst people with stage 3	Real	0.15
rr_stage4_undergone_curative_treatment	rate ratio for stage 4 breast cancer for people with stage 3 breast cancer if had curative treatment at stage 3	Real	0.5
r_death_breast_cancer	probabilty per 3 months of death from breast cancer amongst people with stage 4 breast cancer	Real	0.1
r_breast_lump_discernible_stage1	rate ratio for breast_lump_discernible if have stage 1 breast cancer	Real	0.05
rr_breast_lump_discernible_stage2	rate ratio for breast_lump_discernible if have stage 2 breast cancer	Real	2.0
rr_breast_lump_discernible_stage3	rate ratio for breast_lump_discernible if have stage 3 breast cancer	Real	4.0
rr_breast_lump_discernible_stage4	rate ratio for breast_lump_discernible if have stage 4 breast cancer	Real	10.0
rp_breast_cancer_age3049	relative prevalence at baseline of breast cancer if age3049	Real	20.0
rp_breast_cancer_agege50	relative prevalence at baseline of breast cancer if agege50	Real	20.0
sensitivity_of_biopsy_for_stage1_breast_cancer	sensitivity of biopsy_for diagnosis of stage 1 breast cancer	Real	0.8
sensitivity_of_biopsy_for_stage2_breast_cancer	sensitivity of biopsy_for diagnosis of stage 2 breast cancer	Real	0.95
sensitivity_of_biopsy_for_stage3_breast_cancer	sensitivity of biopsy_for diagnosis of stage 3 breast cancer	Real	0.95
sensitivity_of_biopsy_for_stage4_breast_cancer	sensitivity of biopsy_for diagnosis of stage 4 breast cancer	Real	0.95

CardioMetabolicDisorders

Name	Description	Type	Value
diabetes_onset	all the parameters that specify the linear models for onset of diabetes	Series	…
hypertension_onset	all the parameters that specify the linear models for onset of hypertension	Series	…
chronic_kidney_disease_onset	all the parameters that specify the linear models for onset of chronic_kidney_disease	Series	…
chronic_lower_back_pain_onset	all the parameters that specify the linear models for onset of chronic_lower_back_pain	Series	…
chronic_ischemic_hd_onset	all the parameters that specify the linear models for onset of chronic_ischemic_hd	Series	…
diabetes_removal	all the parameters that specify the linear models for removal of diabetes	Series	…
hypertension_removal	all the parameters that specify the linear models for removal of hypertension	Series	…
chronic_kidney_disease_removal	all the parameters that specify the linear models for removal of chronic_kidney_disease	Series	…
chronic_lower_back_pain_removal	all the parameters that specify the linear models for removal of chronic_lower_back_pain	Series	…
chronic_ischemic_hd_removal	all the parameters that specify the linear models for removal of chronic_ischemic_hd	Series	…
diabetes_hsi	all the parameters that specify diagnostic tests and treatments for diabetes	Series	…
hypertension_hsi	all the parameters that specify diagnostic tests and treatments for hypertension	Series	…
chronic_kidney_disease_hsi	all the parameters that specify diagnostic tests and treatments for chronic_kidney_disease	Series	…
chronic_lower_back_pain_hsi	all the parameters that specify diagnostic tests and treatments for chronic_lower_back_pain	Series	…
chronic_ischemic_hd_hsi	all the parameters that specify diagnostic tests and treatments for chronic_ischemic_hd	Series	…
ever_stroke_onset	all the parameters that specify the linear models for onset of ever_stroke	Series	…
ever_heart_attack_onset	all the parameters that specify the linear models for onset of ever_heart_attack	Series	…
diabetes_death	all the parameters that specify the linear models for death from diabetes	Series	…
hypertension_death	all the parameters that specify the linear models for death from hypertension	Series	…
chronic_kidney_disease_death	all the parameters that specify the linear models for death from chronic_kidney_disease	Series	…
chronic_lower_back_pain_death	all the parameters that specify the linear models for death from chronic_lower_back_pain	Series	…
chronic_ischemic_hd_death	all the parameters that specify the linear models for death from chronic_ischemic_hd	Series	…
ever_stroke_death	all the parameters that specify the linear models for death from ever_stroke	Series	…
ever_heart_attack_death	all the parameters that specify the linear models for death from ever_heart_attack	Series	…
ever_stroke_hsi	all the parameters that specify diagnostic tests and treatments for ever_stroke	Series	…
ever_heart_attack_hsi	all the parameters that specify diagnostic tests and treatments for ever_heart_attack	Series	…
diabetes_initial_prev	initial prevalence of condition	Series	…
hypertension_initial_prev	initial prevalence of condition	Series	…
chronic_kidney_disease_initial_prev	initial prevalence of condition	Series	…
chronic_lower_back_pain_initial_prev	initial prevalence of condition	Series	…
chronic_ischemic_hd_initial_prev	initial prevalence of condition	Series	…
interval_between_polls	months between the main polling event	Integer	3
pr_bmi_reduction	probability of an individual having a reduction in BMI following weight loss treatment	Real	0.1
prob_care_provided_given_seek_emergency_care	The probability that correct care is fully provided to persons that have sought emergency care for a Cardio-metabolic disorder.	Real	0.5

diabetes_onset

value
1.15
0
0
0
0
1
1
1.6
2.21538

Only first 10 rows of 67 are shown.

hypertension_onset

value
0.95
0
0
0
0
0.337838
1.00338
1.00338
1

Only first 10 rows of 67 are shown.

chronic_kidney_disease_onset

value
1.25
0
0
0
0
0.515464
0.515464
0.515464
1

Only first 10 rows of 67 are shown.

chronic_lower_back_pain_onset

value
1
0
0
0
0
0.69
1
1.44615
2.21538

Only first 10 rows of 67 are shown.

chronic_ischemic_hd_onset

value
2.3
0
0
0
0
0.140136
1
1
1

Only first 10 rows of 67 are shown.

diabetes_removal

value
0
0
0
0
0
0
0
0
0

Only first 10 rows of 67 are shown.

hypertension_removal

value
0
0
0
0
0
0
0
0
0

Only first 10 rows of 67 are shown.

chronic_kidney_disease_removal

value
0
0
0
0
0
0
0
0
0

Only first 10 rows of 67 are shown.

chronic_lower_back_pain_removal

value
0.8
0
0
0
0
1
1
1
1

Only first 10 rows of 67 are shown.

chronic_ischemic_hd_removal

value
0
0
0
0
0
0
0
0
0

Only first 10 rows of 67 are shown.

diabetes_hsi

value
216
1
233
0.1
0.42
0.3846
0.8

hypertension_hsi

value
1
221
0.05
0
0.3797
0.8

chronic_kidney_disease_hsi

value
47
1
2064
0
0
0.02
0.8

chronic_lower_back_pain_hsi

value
1
226
0
0
0
0.1

chronic_ischemic_hd_hsi

value
1
226
0
0
0.05
0.8

ever_stroke_onset

value
0.9
0
0
0
0
0.15
0.15
0.15
0.17

Only first 10 rows of 67 are shown.

ever_heart_attack_onset

value
1.5
0
0
0
0
0.05
0.05
0.05
0.05

Only first 10 rows of 67 are shown.

diabetes_death

value
3.2
0
0
0
0
0.2
0.2
0.25
0.25

Only first 10 rows of 67 are shown.

hypertension_death

value
0
0
0
0
0
0
0
0
0

Only first 10 rows of 67 are shown.

chronic_kidney_disease_death

value
2.2
0
0
0
0
0.25
0.2
0.2
0.3

Only first 10 rows of 67 are shown.

chronic_lower_back_pain_death

value
0
0
0
0
0
0
0
0
0

Only first 10 rows of 67 are shown.

chronic_ischemic_hd_death

value
1.4
0
0
0
0
0.673277
0.673277
0.615122
0.641215

Only first 10 rows of 67 are shown.

ever_stroke_death

value
1
0
0
0
0
0.2
0.2
0.35
0.35

Only first 10 rows of 67 are shown.

ever_heart_attack_death

value
1.8
0
0
0
0
0.1
0.1
0.15
0.15

Only first 10 rows of 67 are shown.

ever_stroke_hsi

value
1
226
0
234
0.59

ever_heart_attack_hsi

value
1
226
0
225
0.481

diabetes_initial_prev

value
0
0
0
0.00168696
0.00168696
0.0100913
0.0100913
0.0203044
0.0203044

Only first 10 rows of 42 are shown.

hypertension_initial_prev

value
0
0
0
0.0468696
0.0468696
0.101778
0.101778
0.128891
0.128891

Only first 10 rows of 42 are shown.

chronic_kidney_disease_initial_prev

value
0
0
0
0.0003
0.0003
0.0009
0.0009
0.0033
0.0033

Only first 10 rows of 42 are shown.

chronic_lower_back_pain_initial_prev

value
0.0053
0.0229
0.0341
0.0411
0.0534
0.0657
0.0819
0.0973
0.1095

Only first 10 rows of 42 are shown.

chronic_ischemic_hd_initial_prev

value
0
0
0.0001
0.0005
0.0015
0.0033
0.0065
0.0125
0.0225

Only first 10 rows of 42 are shown.

CareOfWomenDuringPregnancy

Name	Description	Type	Value
prob_seek_anc2	Probability a woman who is not predicted to attended four or more ANC visits will attend ANC2	List	[0.98, 0.98]
prob_seek_anc3	Probability a woman who is not predicted to attended four or more ANC visits will attend ANC3	List	[0.55, 0.55]
prob_seek_anc5	Probability a woman who is predicted to attend four or more ANC visits will attend ANC5	List	[0.125, 0.125]
prob_seek_anc6	Probability a woman who is predicted to attend four or more ANC visits will attend ANC6	List	[0.0625, 0.0625]
prob_seek_anc7	Probability a woman who is predicted to attend four or more ANC visits will attend ANC7	List	[0.03125, 0.03125]
prob_seek_anc8	Probability a woman who is predicted to attend four or more ANC visits will attend ANC8	List	[0.03125, 0.03125]
effect_of_ifa_for_resolving_anaemia	treatment effectiveness of starting iron and folic acid on resolving anaemia	List	[0.7, 0.7]
treatment_effect_blood_transfusion_anaemia	treatment effectiveness of blood transfusion for anaemia in pregnancy	List	[0.9, 0.9]
prob_intervention_delivered_urine_ds	probability a woman will receive the intervention “urine dipstick” given that the HSI has ran and the consumables are available (proxy for clinical quality)	List	[0.53, 0.53]
prob_intervention_delivered_bp	probability a woman will receive the intervention “blood pressure measurement” given that the HSI has ran and the consumables are available (proxy for clinical quality)	List	[0.7, 0.69]
prob_adherent_ifa	probability a woman who is given iron and folic acid will adhere to the treatment for their pregnancy	List	[0.37, 0.34]
prob_intervention_delivered_syph_test	probability a woman will receive the intervention “Syphilis test” given that the HSI has ran and the consumables are available (proxy for clinical quality)	List	[0.43, 0.14]
prob_intervention_delivered_gdm_test	probability a woman will receive the intervention “GDM screening” given that the HSI has ran and the consumables are available (proxy for clinical quality)	List	[0.48, 0.48]
prob_delivery_modes_ec	probabilities that a woman admitted with eclampsia will deliver normally, via caesarean or via assisted vaginal delivery	List	[[0, 0, 1], [0, 0, 1]]
prob_delivery_modes_spe	probabilities that a woman admitted with severe pre-eclampsia will deliver normally, via caesarean or via assisted vaginal delivery	List	[[0.05, 0.05, 0.9], [0.05, 0.05, 0.9]]
sensitivity_bp_monitoring	sensitivity of blood pressure monitoring to detect hypertension	List	[0.74, 0.74]
specificity_bp_monitoring	specificity of blood pressure monitoring to detect hypertension	List	[0.79, 0.79]
sensitivity_urine_protein_1_plus	sensitivity of a urine dipstick test to detect proteinuria at 1+	List	[0.541, 0.541]
specificity_urine_protein_1_plus	specificity of a urine dipstick test to detect proteinuria at 1+	List	[0.841, 0.841]
sensitivity_poc_hb_test	sensitivity of a point of care Hb test to detect anaemia	List	[0.851, 0.851]
specificity_poc_hb_test	specificity of a point of care Hb test to detect anaemia	List	[0.801, 0.801]
sensitivity_fbc_hb_test	sensitivity of a Full Blood Count test to detect anaemia	List	[1.0, 1.0]
specificity_fbc_hb_test	specificity of a Full Blood Count test to detect anaemia	List	[1.0, 1.0]
sensitivity_blood_test_glucose	sensitivity of a blood test to detect raised blood glucose	List	[1.0, 1.0]
specificity_blood_test_glucose	specificity of a blood test to detect raised blood glucose	List	[1.0, 1.0]
sensitivity_blood_test_syphilis	sensitivity of a blood test to detect syphilis	List	[0.82, 0.82]
specificity_blood_test_syphilis	specificity of a blood test to detect syphilis	List	[0.96, 0.96]

Contraception

Name	Description	Type	Value
Method_Use_In_2010	Proportion of women using each method in 2010, by age.	Dataframe	…
Pregnancy_NotUsing_In_2010	Probability per year of a women not on contraceptive becoming pregnant, by age.	Dataframe	…
Pregnancy_NotUsing_HIVeffect	Relative probability of becoming pregnant whilst not using a a contraceptive for HIV-positive women compared to HIV-negative women.	Dataframe	…
Failure_ByMethod	Probability per month of a women on a contraceptive becoming pregnant, by method.	Dataframe	…
rr_fail_under25	The relative risk of becoming pregnant whilst using a contraceptive for woman younger than 25 years compared to older women.	Real	2.2
Initiation_ByMethod	Probability per month of a women who is not using any contraceptive method of starting use of a method, by method.	Dataframe	…
Interventions_Pop	Pop (population scale contraception intervention) intervention multiplier.	Dataframe	…
Interventions_PPFP	PPFP (post-partum family planning) intervention multiplier.	Dataframe	…
Initiation_ByAge	The effect of age on the probability of starting use of contraceptive (add one for multiplicative effect).	Dataframe	…
Initiation_AfterBirth	The probability of a woman starting a contraceptive immidiately after birth, by method.	Dataframe	…
Discontinuation_ByMethod	The probability per month of discontinuing use of a method, by method.	Dataframe	…
Discontinuation_ByAge	The effect of age on the probability of discontinuing use of contraceptive (add one for multiplicative effect).	Dataframe	…
Prob_Switch_From	The probability per month that a women switches from one form of contraceptive to another, conditional that she will not discontinue use of the method.	Dataframe	…
Prob_Switch_From_And_To	The probability of switching to a new method, by method, conditional that the woman will switch to a new method.	Dataframe	…
days_between_appts_for_maintenance	The number of days between successive family planning appointments for women that are maintaining the use of a method (for each method insorted(self.states_that_may_require_HSI_to_maintain_on), i.e.[IUD, implant, injections, other_modern, pill]).	List	[4383, 1461, 91, 91, 91, 91]
age_specific_fertility_rates	Data table from official source (WPP) for age-specific fertility rates and calendar period.	Dataframe	…
scaling_factor_on_monthly_risk_of_pregnancy	Scaling factor (by age-group: 15-19, 20-24, …, 45-49) on the monthly risk of pregnancy and contraceptive failure rate. This value is found through calibration so that, at the beginning of the simulation, the age-specific monthly probability of a woman having a live birth matches the WPP age-specific fertility rate value for the same year.	List	[1.227, 0.7191, 0.6632, 0.84945, 0.86135, 0.645, 0.941]
max_number_of_runs_of_hsi_if_consumable_not_available	The maximum number of time an HSI can run (repeats occur if the consumables are not available).	Integer	1000
max_days_delay_between_decision_to_change_method_and_hsi_scheduled	The maximum delay (in days) between the decision for a contraceptive to change and the topen date of the HSI that is scheduled to effect the change (when using the healthsystem).	Integer	7
use_interventions	if True: FP interventions (pop & ppfp) are simulated from the date ‘interventions_start_date’, if False: FP interventions (pop & ppfp) are not simulated.	Boolean	False
interventions_start_date	The date since which the FP interventions (pop & ppfp) are implemented, if at all (ie, if use_interventions==True	Date	2023-01-01 00:00:00

Method_Use_In_2010

age	not_using	pill	IUD	injections	implant	male_condom	female_sterilization	other_modern	periodic_abstinence	withdrawal	other_traditional
16	0.956447	0	0.000853971	0.0187874	0	0.0204953	0	0	0.00256191	0	0.000853971
17	0.917373	0.00105932	0	0.0413136	0	0.0275424	0	0	0.00317797	0.00741525	0.00105932
18	0.843715	0.00679502	0	0.103058	0	0.0396376	0	0	0	0.00566251	0
19	0.738693	0.0188442	0	0.182161	0	0.0376884	0	0	0.00125628	0.0138191	0.00251256
20	0.693305	0.0107991	0	0.218143	0	0.0410367	0.00431965	0	0.00215983	0.0215983	0.00323974
21	0.644362	0.0173482	0.00123916	0.272615	0	0.0371747	0.00123916	0	0.00123916	0.00743494	0.00619579
22	0.634744	0.018931	0	0.26392	0	0.0356347	0.00445434	0	0.00556793	0.0155902	0.00668151
23	0.642616	0.00676437	0.00225479	0.264938	0	0.0394588	0.00338219	0	0.00789177	0.0124014	0.00676437
24	0.588101	0.020595	0.00114416	0.286041	0	0.0297483	0.0125858	0	0.00800915	0.0228833	0.00915332

Only first 10 rows of 35 are shown.

Pregnancy_NotUsing_In_2010

age	AnnualProb
16	0.0780862
17	0.148498
18	0.298088
19	0.402345
20	0.532862
21	0.552413
22	0.586474
23	0.569371
24	0.598742

Only first 10 rows of 35 are shown.

Pregnancy_NotUsing_HIVeffect

age_	RR_pregnancy
16	1.4
17	1.4
18	1.4
19	1.4
20	0.9
21	0.9
22	0.9
23	0.9
24	0.9

Only first 10 rows of 35 are shown.

Failure_ByMethod

pill	IUD	injections	implant	male_condom	female_sterilization	other_modern	periodic_abstinence	withdrawal	other_traditional
0.00192848	0	0.000530667	9.50789e-05	0.00117109	0	0	0.000552797	0.00358032	0.004923

Initiation_ByMethod

not_using	pill	IUD	injections	implant	male_condom	female_sterilization	other_modern	periodic_abstinence	withdrawal	other_traditional
0.993934	0.000397942	1.84759e-05	0.00382829	0.000117488	0.000793041	0.000274295	2.5582e-05	9.2853e-05	0.000358621	0.000159177

Interventions_Pop

pill	IUD	injections	implant	male_condom	female_sterilization	other_modern	periodic_abstinence	withdrawal	other_traditional
2.5	11	1.6	8	2.6	2	5	1	1	1

Interventions_PPFP

pill	IUD	injections	implant	male_condom	female_sterilization	other_modern	periodic_abstinence	withdrawal	other_traditional
2.5	11	1.6	8	2.6	2	5	1	1	1

Initiation_ByAge

age	r_init1_age
16	0.224538
17	0.147192
18	0.089718
19	0.0469456
20	0.0151724
21	-0.00829227
22	-0.0254293
23	-0.0377144
24	-0.0462588

Only first 10 rows of 35 are shown.

Initiation_AfterBirth

not_using	pill	IUD	injections	implant	male_condom	female_sterilization	other_modern	periodic_abstinence	withdrawal	other_traditional
0.99654	0.000224019	5.84398e-06	0.00180189	5.06478e-05	0.000210383	0.000718809	1.1688e-05	0.000105192	0.000181163	0.000149995

Discontinuation_ByMethod

pill	IUD	injections	implant	male_condom	female_sterilization	other_modern	periodic_abstinence	withdrawal	other_traditional
0.0496232	0.0111009	0.0333511	0.00627062	0.0503725	0	0.0332874	0.0422692	0.0423377	0.0497931

Discontinuation_ByAge

age	r_discont_age
16	-0.628712
17	-0.438627
18	-0.29471
19	-0.185198
20	-0.101633
21	-0.037841
22	0.0107489
23	0.0475587
24	0.0751794

Only first 10 rows of 35 are shown.

Prob_Switch_From

pill	IUD	injections	implant	male_condom	female_sterilization	other_modern	periodic_abstinence	withdrawal	other_traditional
0.0109093	0.00145124	0.0030322	0.000862686	0.0114341	0	0.00265503	0.00751371	0.0137878	0.027214

Prob_Switch_From_And_To

switchfrom	pill	IUD	injections	implant	male_condom	female_sterilization	other_modern	periodic_abstinence	withdrawal	other_traditional
pill	0	0	0.540323	0.217742	0.104839	0.0564516	0.0241935	0.00806452	0.0403226	0.00806452
IUD	0.125	0	0.375	0.25	0.125	0.125	0	0	0	0
injections	0.262806	0.0267261	0	0.447661	0.106904	0.0757238	0.00890869	0.00890869	0.0445434	0.0178174
implant	0.205882	0.0294118	0.632353	0	0.102941	0.0294118	0	0	0	0
male_condom	0.0829268	0.00487805	0.595122	0.22439	0	0.0292683	0.00487805	0.0097561	0.0487805	0
other_modern	0	0	1	0	0	0	0	0	0	0
periodic_abstinence	0	0	0.333333	0.666667	0	0	0	0	0	0
withdrawal	0.037037	0.0185185	0.518519	0.296296	0.111111	0.0185185	0	0	0	0
other_traditional	0	0	0.73913	0.144928	0.057971	0.057971	0	0	0	0

age_specific_fertility_rates

Variant	Period	Age_Grp	asfr
WPP_Estimates	1955-1959	15-19	0.183883
WPP_Estimates	1960-1964	15-19	0.186647
WPP_Estimates	1965-1969	15-19	0.191979
WPP_Estimates	1970-1974	15-19	0.197259
WPP_Estimates	1975-1979	15-19	0.202538
WPP_Estimates	1980-1984	15-19	0.202538
WPP_Estimates	1985-1989	15-19	0.193211
WPP_Estimates	1990-1994	15-19	0.159343
WPP_Estimates	1995-1999	15-19	0.160904

Only first 10 rows of 434 are shown.

Copd

Name	Description	Type	Value
prob_mod_exacerb	probability of moderate exacerbation given lung function, for each lung function category.	List	[0, 0, 0, 0.01, 0.05, 0.2, 0.3]
prob_sev_exacerb	probability of severe exacerbation given lung function, for each lung function category.	List	[0, 0, 0, 0.0, 0.0, 0.05, 0.1]
prob_progress_to_next_cat	probability of changing from a lower lung function category to a higher lung function category	Real	0.015
prob_will_die_sev_exacerbation_ge80	probability that a person equal to or greater than 80 years will die of severe exacerbation	Real	0.95
prob_will_die_sev_exacerbation_7079	probability that a person between 70 to 79 years will die of severe exacerbation	Real	0.7
prob_will_die_sev_exacerbation_6069	probability that a person between 60 to 99 years will die of severe exacerbation	Real	0.5
prob_will_die_sev_exacerbation_5059	probability that a person between 50 to 59 years will die of severe exacerbation	Real	0.05
prob_will_die_sev_exacerbation_4049	probability that a person between 40 to 49 years will die of severe exacerbation	Real	0.02
prob_will_die_sev_exacerbation_3039	probability that a person between 30 to 39 years will die of severe exacerbation	Real	0.01
prob_will_die_sev_exacerbation_lt30	probability that a person less than 30 years will die of severe exacerbation	Real	0.0
eff_oxygen	the effect of oxygen on individuals with severe exacerbation	Real	0.6
rel_risk_progress_per_higher_cat	relative risk of progression to the next higher level of lung function for each higher level	Real	0.5
rel_risk_tob	relative effect of tobacco on the rate of lung function progression	Real	7.0
rel_risk_wood_burn_stove	relative risk of wood burn stove on the rate of lung function progression	Real	2.0
prob_not_tob_lung_func_15_39	probability of lung function categories in individuals aged 15-39 and do not smoke tobacco	List	[0.496396, 0.337947, 0.114555, 0.040078, 0.010086, 0.000938, 0.0]
prob_not_tob_lung_func_40_59	probability of lung function categories in individuals aged 40-59 and do not smoke tobacco	List	[0.114194, 0.306129, 0.292286, 0.212143, 0.067501, 0.007387, 0.00036]
prob_not_tob_lung_func_gr59	probability of lung function categories in individuals aged 60+ and do not smoke tobacco	List	[0.009201, 0.08707, 0.263341, 0.44523, 0.183632, 0.010073, 0.001453]
prob_tob_lung_func_15_39	probability of lung function categories in individuals aged 15-39 who smoke tobacco	List	[0.06712, 0.199903, 0.259728, 0.241245, 0.148346, 0.071498, 0.01216]
prob_tob_lung_func_40_59	probability of lung function categories in individuals aged 40-59 who smoke tobacco	List	[0.001499, 0.033733, 0.112819, 0.231259, 0.337331, 0.225637, 0.057722]
prob_tob_lung_func_gr59	probability of lung function categories in individuals aged 60+ who smoke tobacco	List	[0.0, 0.0, 0.035366, 0.20122, 0.453659, 0.246341, 0.063414]

Demography

Name	Description	Type	Value
max_age_initial	The oldest age (in whole years) in the initial population	Integer	120
pop_2010	Population in 2010 for initialising population	Dataframe	…
district_num_to_district_name	Mapping from district_num to district name	Dictionary	…
district_num_to_region_name	Mapping from district_num to region name	Dictionary	…
districts_in_region	Set of districts (by name) that are within a region (by name)	Dictionary	…
all_cause_mortality_schedule	All-cause age-specific mortality rates from WPP	Dataframe	…
fraction_of_births_male	Birth Sex Ratio	Series	…

pop_2010

District	District_Num	Region	Sex	Age	Count
Chitipa	0	Northern	M	1	3673.51
Chitipa	0	Northern	M	2	3538.09
Chitipa	0	Northern	M	3	3410.42
Chitipa	0	Northern	M	4	3289.97
Chitipa	0	Northern	M	5	3176.2
Chitipa	0	Northern	M	6	3068.58
Chitipa	0	Northern	M	7	2966.6
Chitipa	0	Northern	M	8	2869.74
Chitipa	0	Northern	M	9	2777.45

Only first 10 rows of 6464 are shown.

district_num_to_district_name

0	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31
Chitipa	Karonga	Nkhata Bay	Rumphi	Mzimba	Likoma	Mzuzu City	Kasungu	Nkhotakota	Ntchisi	Dowa	Salima	Lilongwe	Mchinji	Dedza	Ntcheu	Lilongwe City	Mangochi	Machinga	Zomba	Chiradzulu	Blantyre	Mwanza	Thyolo	Mulanje	Phalombe	Chikwawa	Nsanje	Balaka	Neno	Zomba City	Blantyre City

district_num_to_region_name

0	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31
Northern	Northern	Northern	Northern	Northern	Northern	Northern	Central	Central	Central	Central	Central	Central	Central	Central	Central	Central	Southern	Southern	Southern	Southern	Southern	Southern	Southern	Southern	Southern	Southern	Southern	Southern	Southern	Southern	Southern

districts_in_region

Northern

0	1	2	3	4	5	6
Chitipa	Mzimba	Likoma	Mzuzu City	Nkhata Bay	Karonga	Rumphi

Central

0	1	2	3	4	5	6	7	8	9
Mchinji	Ntchisi	Dedza	Lilongwe	Lilongwe City	Dowa	Nkhotakota	Salima	Ntcheu	Kasungu

Southern

0	1	2	3	4	5	6	7	8	9	10	11	12	13	14
Neno	Chikwawa	Zomba City	Blantyre	Phalombe	Thyolo	Mwanza	Mangochi	Machinga	Mulanje	Balaka	Chiradzulu	Zomba	Blantyre City	Nsanje

all_cause_mortality_schedule

fallbackyear	sex	age_years	death_rate
1950	M	1	0.0572109
1950	M	2	0.0572109
1950	M	3	0.0572109
1950	M	4	0.0572109
1950	M	5	0.0139565
1950	M	6	0.0139565
1950	M	7	0.0139565
1950	M	8	0.0139565
1950	M	9	0.0139565

Only first 10 rows of 7200 are shown.

fraction_of_births_male

frac_births_male
0.50495
0.50495
0.50495
0.50495
0.50495
0.50495
0.50495
0.50495
0.50495

Only first 10 rows of 150 are shown.

Depression

Name	Description	Type	Value
init_pr_depr_m_age1519_no_cc_wealth123	Initial probability of being depressed in male age1519 with no chronic condition with wealth level 1 or 2 or 3	Real	0.06
init_rp_depr_f_not_rec_preg	Initial relative prevalence of being depressed in females not recently pregnant	Real	1.5
init_rp_depr_f_rec_preg	Initial relative prevalence of being depressed in females recently pregnant	Real	3.0
init_rp_depr_age2059	Initial relative prevalence of being depressed in 20-59 year olds vs 15-19	Real	1.0
init_rp_depr_agege60	Initial relative prevalence of being depressed in 60+ year olds vs 15-19	Real	3.0
init_rp_depr_cc	Initial relative prevalence of being depressed in people with chronic condition	Real	1.0
init_rp_depr_wealth45	Initial relative prevalence of being depressed in people with wealth level 4 or 5 vs 1 or 2 or 3	Real	1.0
init_rp_ever_depr_per_year_older_m	Initial relative prevalence ever depression per year older in men	Real	0.004
init_rp_ever_depr_per_year_older_f	Initial relative prevalence ever depression per year older in women	Real	0.006
init_pr_ever_talking_therapy_if_diagnosed	Initial probability of ever having had talking therapy if ever diagnosed with depression	Real	1.0
init_pr_antidepr_curr_depr	Initial probability of being on antidepressants if currently depressed	Real	0.11
init_rp_antidepr_ever_depr_not_curr	Initial relative prevalence of being on antidepressants if ever depressed but not currently	Real	0.5
init_pr_ever_diagnosed_depression	Initial probability of having ever been diagnosed with depression, amongst people with ever depression and not on antidepressants	Real	0.2
init_pr_ever_self_harmed_if_ever_depr	Initial probability of having ever self harmed if ever depressed	Real	0.004
base_3m_prob_depr	Probability of onset of depression in a 3 month period if male, wealth 1 2 or 3, no chronic condition and never previously depressed	Real	0.0021
rr_depr_wealth45	Relative rate of depression when in wealth level 4 or 5 vs 1 or 2 or 3	Real	3.0
rr_depr_cc	Relative rate of depression if has any chronic disease	Real	1.25
rr_depr_pregnancy	Relative rate of depression when pregnant or recently pregnant	Real	3.0
rr_depr_female	Relative rate of depression for females vs males	Real	1.5
rr_depr_prev_epis	Relative rate of depression associated with previous depression vs never previously depressed	Real	50.0
rr_depr_on_antidepr	Relative rate of depression episode if on antidepressants	Real	30.0
rr_depr_age1519	Relative rate of depression associated with 15-20 year olds	Real	1.0
rr_depr_agege60	Relative rate of depression associated with age > 60	Real	3.0
rr_depr_hiv	Relative rate of depression associated with HIV infection	Real	1.99
depr_resolution_rates	Risk of depression resolving in 3 months if no chronic conditions and no treatments.Each individual is equally likely to be assigned each of these risks	List	[0.2, 0.3, 0.5, 0.7, 0.95]
rr_resol_depr_cc	Relative rate of resolving depression if has any chronic disease	Real	0.5
rr_resol_depr_on_antidepr	Relative rate of resolving depression if on antidepressants	Real	1.5
rr_resol_depr_current_talk_ther	Relative rate of resolving depression if has ever had talking therapy vs has never had talking therapy	Real	1.1
prob_3m_stop_antidepr	Probability per 3 months of stopping antidepressants when not currently depressed.	Real	0.7
prob_3m_default_antidepr	Probability per 3 months of stopping antidepressants when still depressed.	Real	0.2
prob_3m_suicide_depr_m	Probability per 3 months of suicide in currently depressed men	Real	0.0005
rr_suicide_depr_f	Relative risk of suicide in women compared with men	Real	0.333
prob_3m_selfharm_depr	Probability per 3 months of non-fatal self harm in those currently depressed	Real	0.0005
sensitivity_of_assessment_of_depression	The sensitivity of the clinical assessment in detecting the true current status of depression	Real	0.75
pr_assessed_for_depression_in_generic_appt_level1	Probability that a person is assessed for depression during a non-emergency generic appointmentlevel 1	Real	0.01
anti_depressant_medication_item_code	The item code used for one month of anti-depressant treatment	Integer	267
pr_assessed_for_depression_for_perinatal_female	Probability that a perinatal female is assessed for depression during antenatal or postnatal services	Real	0.01

Diarrhoea

Name	Description	Type	Value
base_inc_rate_diarrhoea_by_rotavirus	incidence rate (per person-year) of diarrhoea caused by rotavirus in age groups 0-11, 12-23, 24-59 months	List	[0.175245863, 0.097007598, 0.009324]
base_inc_rate_diarrhoea_by_shigella	incidence rate (per person-year) of diarrhoea caused by shigella spp in age groups 0-11, 12-23, 24-59 months	List	[0.117936461999999, 0.078794104, 0.093018]
base_inc_rate_diarrhoea_by_adenovirus	incidence rate (per person-year) of diarrhoea caused by adenovirus 40/41 in age groups 0-11, 12-23, 24-59 months	List	[0.0586618, 0.058661803, 0.006438]
base_inc_rate_diarrhoea_by_cryptosporidium	incidence rate (per person-year) of diarrhoea caused by cryptosporidium in age groups 0-11, 12-23, 24-59 months	List	[0.030886699, 0.0117923629999999, 0.004662]
base_inc_rate_diarrhoea_by_campylobacter	incidence rate (per person-year) of diarrhoea caused by campylobacter spp in age groups 0-11, 12-23, 24-59 months	List	[0.098663257, 0.027915478, 0.004884]
base_inc_rate_diarrhoea_by_ETEC	incidence rate (per person-year) of diarrhoea caused by ETEC in age groups 0-11, 12-23, 24-59 months	List	[0.27925146, 0.170477152, 0.019758]
base_inc_rate_diarrhoea_by_sapovirus	incidence rate (per person-year) of diarrhoea caused by sapovirus in age groups 0-11, 12-23, 24-59 months	List	[0.100972179, 0.132603114, 0.00555]
base_inc_rate_diarrhoea_by_norovirus	incidence rate (per person-year) of diarrhoea caused by norovirus in age groups 0-11, 12-23, 24-59 months	List	[0.204864004, 0.066146727, 0.000888]
base_inc_rate_diarrhoea_by_astrovirus	incidence rate (per person-year) of diarrhoea caused by astrovirus in age groups 0-11, 12-23, 24-59 months	List	[0.054208352, 0.035974076, 0.001332]
base_inc_rate_diarrhoea_by_tEPEC	incidence rate (per person-year) of diarrhoea caused by tEPEC in age groups 0-11, 12-23, 24-59 months	List	[0.0608224569999999, 0.022716889, 0.001998]
rr_diarrhoea_HHhandwashing	relative rate of diarrhoea with household handwashing with soap	Real	0.7
rr_diarrhoea_improved_sanitation	relative rate of diarrhoea for improved sanitation	Real	0.75
rr_diarrhoea_clean_water	relative rate of diarrhoea for access to clean drinking water	Real	0.67
rr_diarrhoea_exclusive_vs_partial_breastfeeding_<6mo	relative rate of diarrhoea for partial breastfeeding in <6 months old, compared to exclusive breastfeeding	Real	1.68
rr_diarrhoea_exclusive_vs_no_breastfeeding_<6mo	relative rate of diarrhoea for no breastfeeding in <6 months old, compared to exclusive breastfeeding	Real	2.65
rr_diarrhoea_any_vs_no_breastfeeding_6_11mo	relative rate of diarrhoea for no breastfeeding in 6 months old to 1 years old, compared to any breastfeeding at this age group	Real	1.32
rr_diarrhoea_untreated_HIV	relative rate of diarrhoea for HIV positive status	Real	5.4
rr_diarrhoea_SAM	relative rate of diarrhoea for severe malnutrition	Real	1.2
proportion_AWD_in_rotavirus	acute diarrhoea type caused in rotavirus-attributed diarrhoea	Real	0.97668
proportion_AWD_in_shigella	acute diarrhoea type caused in shigella-attributed diarrhoea	Real	0.861942
proportion_AWD_in_adenovirus	acute diarrhoea type caused in adenovirus-attributed diarrhoea	Real	0.950061
proportion_AWD_in_cryptosporidium	acute diarrhoea type caused in cryptosporidium-attributed diarrhoea	Real	0.970984
proportion_AWD_in_campylobacter	acute diarrhoea type caused in campylobacter-attributed diarrhoea	Real	0.896768
proportion_AWD_in_ETEC	acute diarrhoea type caused in ETEC-attributed diarrhoea	Real	0.950465
proportion_AWD_in_sapovirus	acute diarrhoea type caused in sapovirus-attributed diarrhoea	Real	0.966385
proportion_AWD_in_norovirus	acute diarrhoea type caused in norovirus-attributed diarrhoea	Real	0.961643
proportion_AWD_in_astrovirus	acute diarrhoea type caused in astrovirus-attributed diarrhoea	Real	0.974147
proportion_AWD_in_tEPEC	acute diarrhoea type in tEPEC-attributed diarrhoea	Real	0.961485
prob_dehydration_by_rotavirus	probability of any dehydration caused by rotavirus	Real	0.153093
prob_dehydration_by_shigella	probability of any dehydration caused by shigella	Real	0.102962
prob_dehydration_by_adenovirus	probability of any dehydration caused by adenovirus	Real	0.079524
prob_dehydration_by_cryptosporidium	probability of any dehydration caused by cryptosporidium	Real	0.121458
prob_dehydration_by_campylobacter	probability of any dehydration caused by campylobacter	Real	0.072808
prob_dehydration_by_ETEC	probability of any dehydration caused by ETEC	Real	0.075925
prob_dehydration_by_sapovirus	probability of any dehydration caused by sapovirus	Real	0.10364
prob_dehydration_by_norovirus	probability of any dehydration caused by norovirus	Real	0.090728
prob_dehydration_by_astrovirus	probability of any dehydration caused by astrovirus	Real	0.122776
prob_dehydration_by_tEPEC	probability of any dehydration caused by tEPEC	Real	0.113362
probability_of_severe_dehydration_if_some_dehydration	probability that someone with diarrhoea and some dehydration develops severe dehydration	Real	0.167
prob_prolonged_diarr_rotavirus	probability of prolonged episode in rotavirus-attributed diarrhoea	Real	0.117706
prob_prolonged_diarr_shigella	probability of prolonged episode by shigella-attributed diarrhoea	Real	0.165342
prob_prolonged_diarr_adenovirus	probability of prolonged episode by adenovirus-attributed diarrhoea	Real	0.116406
prob_prolonged_diarr_cryptosporidium	probability of prolonged episode by cryptosporidium-attributed diarrhoea	Real	0.169134
prob_prolonged_diarr_campylobacter	probability of prolonged episode by campylobacter-attributed diarrhoea	Real	0.152206
prob_prolonged_diarr_ETEC	probability of prolonged episode by ETEC-attributed diarrhoea	Real	0.114177
prob_prolonged_diarr_sapovirus	probability of prolonged episode by sapovirus-attributed diarrhoea	Real	0.133209
prob_prolonged_diarr_norovirus	probability of prolonged episode by norovirus-attributed diarrhoea	Real	0.118223
prob_prolonged_diarr_astrovirus	probability of prolonged episode by norovirus-attributed diarrhoea	Real	0.13511
prob_prolonged_diarr_tEPEC	probability of prolonged episode by tEPEC-attributed diarrhoea	Real	0.190845
prob_prolonged_to_persistent_diarr	probability of prolonged diarrhoea becoming persistent diarrhoea	Real	0.2866
rr_bec_persistent_age>6mo	relative rate of acute diarrhoea becoming persistent diarrhoea for children over 6 months	Real	0.26
rr_bec_persistent_HIV	relative rate of acute diarrhoea becoming persistent diarrhoea for HIV positive	Real	1.7
rr_bec_persistent_SAM	relative rate of acute diarrhoea becoming persistent diarrhoea for severely acute malnutrition	Real	1.7
rr_bec_persistent_stunted	relative rate of acute diarrhoea becoming persistent diarrhoea for stunted children	Real	33.3
min_dur_acute	The minimum duration (in days) for an episode that is classified as an acute episode	Integer	1
min_dur_prolonged	The minimum duration (in days) for an episode that is classified as a prolonged episode	Integer	5
min_dur_persistent	The minimum duration (in days) for an episode that is classified as a persistent episode	Integer	13
max_dur_persistent	The maximum duration (in days) for an episode that is classified as a persistent episode	Integer	30
prob_fever_by_rotavirus	probability of fever caused by rotavirus	Real	0.384925
prob_fever_by_shigella	probability of fever caused by shigella	Real	0.319876
prob_fever_by_adenovirus	probability of fever caused by adenovirus	Real	0.271513
prob_fever_by_cryptosporidium	probability of fever caused by cryptosporidium	Real	0.322385
prob_fever_by_campylobacter	probability of fever caused by campylobacter	Real	0.312807
prob_fever_by_ETEC	probability of fever caused by ETEC	Real	0.258931
prob_fever_by_sapovirus	probability of fever caused by sapovirus	Real	0.292276
prob_fever_by_norovirus	probability of fever caused by norovirus	Real	0.251071
prob_fever_by_astrovirus	probability of fever caused by astrovirus	Real	0.195905
prob_fever_by_tEPEC	probability of fever caused by tEPEC	Real	0.384547
prob_vomiting_by_rotavirus	probability of vomiting caused by rotavirus	Real	0.471793
prob_vomiting_by_shigella	probability of vomiting caused by shigella	Real	0.209852
prob_vomiting_by_adenovirus	probability of vomiting caused by adenovirus	Real	0.308677
prob_vomiting_by_cryptosporidium	probability of vomiting caused by cryptosporidium	Real	0.243581
prob_vomiting_by_campylobacter	probability of vomiting caused by campylobacter	Real	0.218669
prob_vomiting_by_ETEC	probability of vomiting caused by ETEC	Real	0.283139
prob_vomiting_by_sapovirus	probability of vomiting caused by sapovirus	Real	0.303154
prob_vomiting_by_norovirus	probability of vomiting caused by norovirus	Real	0.299343
prob_vomiting_by_astrovirus	probability of vomiting caused by astrovirus	Real	0.276018
prob_vomiting_by_tEPEC	probability of vomiting caused by tEPEC	Real	0.285661
adjustment_factor_on_cfr	Factor by which fatality probabilities are multiplied (to be used in calibration)	Real	3.75
case_fatality_rate_AWD	case fatality rate for acute watery diarrhoea cases	Real	0.0015
rr_diarr_death_bloody	relative risk of diarrhoea death (compared to case_fatality_rate_AWD if the diarrhoea is of type “bloody” (i.e. dyssentry).	Real	7.6
rr_diarr_death_age24to59mo	relative risk of diarrhoea death for ages 24 to 59 months	Real	0.38
rr_diarr_death_if_duration_longer_than_13_days	relative risk of diarrhoea death if the duration episode is 13 days or longer	Real	0.0035
rr_diarr_death_severe_dehydration	relative risk of diarrhoea death for cases with severe dehyadration	Real	3.45
rr_diarr_death_untreated_HIV	relative risk of diarrhoea death for untreated HIV	Real	5.05
rr_diarr_death_SAM	relative risk of diarrhoea death for severe acute malnutrition	Real	4.13
rr_diarr_death_alri	relative risk of diarrhoea death if concurrent lower respiratory infection	Real	3.51
rr_diarr_death_cryptosporidium	relative risk of diarrhoea death if caused by cryptosporidium	Real	2.14
rr_diarr_death_shigella	relative risk of diarrhoea death if caused by shigella	Real	2.8
sensitivity_severe_dehydration_visual_inspection	sensitivity of IMCI severe dehydration algorithm for dehydration >9% loss of body weight	Real	0.77
specificity_severe_dehydration_visual_inspection	specificity of IMCI severe dehydration algorithm for dehydration >9% loss of body weight	Real	0.67
prob_hospitalization_on_danger_signs	probability of hospitalisation when danger signs are detected in an initial consultation	Real	0.7
prob_WHOPlanC_cures_dehydration_if_severe_dehydration	probability that severe dehydration is cured by Treatment Plan C	Real	0.9
prob_ORS_cures_dehydration_if_severe_dehydration	probability that severe dehydration is cured by ORS	Real	0.721
prob_ORS_cures_dehydration_if_non_severe_dehydration	probability that non-severe dehydration is cured by ORS	Real	0.93
prob_antibiotic_cures_dysentery	probability that blood-in-stool is removed by the use of antibiotics	Real	0.99
number_of_days_reduced_duration_with_zinc	number of days reduced duration with zinc	Integer	1
days_between_treatment_and_cure	number of days between any treatment being given in an HSI and the cure occurring.	Integer	5
rr_severe_dehydration_due_to_rotavirus_with_R1_under1yo	relative risk of severe dehydration with rotavirus vaccine, for under 1 years old.	Real	0.63
rr_severe_dehydration_due_to_rotavirus_with_R1_over1yo	relative risk of severe dehydration with rotavirus vaccine, for those aged 1 year and older.	Real	0.35

Epi

Name	Description	Type	Value
baseline_coverage	baseline vaccination coverage (all vaccines)	Dataframe	…
vaccine_schedule	vaccination schedule applicable from 2018 onwards	Series	…
prob_facility_level_for_vaccine	The probability of going to each facility-level (0 / 1a / 1b / 2) for child having vaccines given through childhood immunisation schedule. The probabilities must sum to 1.0	List	[0, 0.8, 0.1, 0.1]

baseline_coverage

Year	BCG	DTP1	DTP3	HepB3	Hib3	MCV1	MCV2	PCV3	Pol3	RCV1	Rota	IPV1	AgeOn01Jan2010
1981	0.86	0.86	0.66	0	0	0.64	0	0	0.57	0	0	0	28
1982	0.87	0.84	0.64	0	0	0.64	0	0	0.58	0	0	0	27
1983	0.81	0.84	0.63	0	0	0.58	0	0	0.58	0	0	0	26
1984	0.74	0.8	0.58	0	0	0.5	0	0	0.56	0	0	0	25
1985	0.87	0.78	0.55	0	0	0.49	0	0	0.55	0	0	0	24
1986	0.87	0.8	0.57	0	0	0.6	0	0	0.53	0	0	0	23
1987	0.92	0.92	0.78	0	0	0.79	0	0	0.78	0	0	0	22
1988	0.9	0.94	0.82	0	0	0.82	0	0	0.72	0	0	0	21
1989	0.96	0.95	0.87	0	0	0.84	0	0	0.9	0	0	0	20

Only first 10 rows of 42 are shown.

vaccine_schedule

date_administration_days
1
42
70
98
42
70
98
42
70

Only first 10 rows of 21 are shown.

Epilepsy

Name	Description	Type	Value
init_epil_seiz_status	Proportions in each seizure status category at baseline	List	[0.974, 0.0175, 0.007, 0.0015]
init_prop_antiepileptic_seiz_stat_1	initial proportions on antiepileptic by if seizure status = 1	Real	0.15
init_prop_antiepileptic_seiz_stat_2	initial proportions on antiepileptic by if seizure status = 2	Real	0.15
init_prop_antiepileptic_seiz_stat_3	initial proportions on antiepileptic by if seizure status = 3	Real	0.2
base_3m_prob_epilepsy	base probability of epilepsy per 3 month period if age < 20	Real	0.000178
rr_epilepsy_age_ge20	relative rate of epilepsy if age over 20	Real	0.3
prop_inc_epilepsy_seiz_freq	proportion of incident epilepsy cases with frequent seizures	Real	0.1
base_prob_3m_seiz_stat_freq_infreq	base probability per 3 months of seizure status frequent if current infrequent	Real	0.05
rr_effectiveness_antiepileptics	relative rate of seizure status frequent if current infrequent if on antiepileptic	Real	3.0
base_prob_3m_seiz_stat_infreq_freq	base probability per 3 months of seizure status infrequent if current frequent	Real	0.05
base_prob_3m_seiz_stat_infreq_none	base probability per 3 months of seizure status infrequent if current nonenow	Real	0.05
base_prob_3m_seiz_stat_none_freq	base probability per 3 months of seizure status nonenow if current frequent	Real	0.05
base_prob_3m_seiz_stat_none_infreq	base probability per 3 months of seizure status nonenow if current infrequent	Real	0.05
base_prob_3m_stop_antiepileptic	base probability per 3 months of stopping antiepileptic, if nonenow seizures	Real	0.1
rr_stop_antiepileptic_seiz_infreq_or_freq	relative rate of stopping antiepileptic if infrequent or frequent seizures	Real	0.5
base_prob_3m_epi_death	base probability per 3 months of epilepsy death	Real	0.000568
daly_wt_epilepsy_severe	disability weight for severe epilepsycontrolled phase - code 860	Real	0.552
daly_wt_epilepsy_less_severe	disability weight for less severe epilepsycontrolled phase - code 861	Real	0.263
daly_wt_epilepsy_seizure_free	disability weight for less severe epilepsycontrolled phase - code 862	Real	0.049
prob_start_anti_epilep_when_seizures_detected_in_generic_first_appt	probability that someone who has had a seizure is started on anti-epileptics. This is calibrated to induce the correct proportion of persons with epilepsy currently receiving anti-epileptics.	Real	0.4
max_num_of_failed_attempts_before_defaulting	maximum number of time an HSI can be repeated if the relevant essential consumables are not available.	Integer	2

HealthSeekingBehaviour

Name	Description	Type	Value
force_any_symptom_to_lead_to_healthcareseeking	Whether every symptom [except those that declare they should not lead to any healthcare seeking] should always lead to healthcare seeking immediately.	Boolean	False
prob_non_emergency_care_seeking_by_level	The probability of going to each facility-level when non-emergency care is sought. The values in the list are the probabilities of going to facility level 0 / 1a / 1b / 2, respectively, and these values must sum to 1.0.	List	[0.14, 0.66, 0.08, 0.12]
baseline_odds_of_healthcareseeking_children	odds of health-care seeking (children: 0-14) if male, 0-5 years-old, living in a rural setting in the Northern region, and not in the wealth categories 4 or 5	Real	2.17
odds_ratio_children_sex_Female	odds ratio for health-care seeking (children) if sex is Female	Real	1.12
odds_ratio_children_age_5to14	odds ratio for health-care seeking (children) if aged 5-14	Real	0.5
odds_ratio_children_setting_urban	odds ratio for health-care seeking (children) if setting is Urban	Real	1.75
odds_ratio_children_region_Central	odds ratio for health-care seeking (children) if region is Central	Real	0.43
odds_ratio_children_region_Southern	odds ratio for health-care seeking (children) if region is Southern	Real	0.56
odds_ratio_children_wealth_higher	odds ratio for health-care seeking (children) if wealth is in categories 4 or 5	Real	1.9
baseline_odds_of_healthcareseeking_adults	odds of health-care seeking (adults: 15+) if male, 15-34 year-olds, living in a rural setting in the Northern region, and not in the wealth categories 4 or 5.	Real	1.27
odds_ratio_adults_sex_Female	odds ratio for health-care seeking (adults) if sex is Female	Real	1.28
odds_ratio_adults_age_35to59	odds ratio for health-care seeking (adults) if aged 35-59	Real	0.93
odds_ratio_adults_age_60plus	odds ratio for health-care seeking (adults) if aged 60+	Real	0.94
odds_ratio_adults_setting_urban	odds ratio for health-care seeking (adults) if setting is Urban	Real	1.67
odds_ratio_adults_region_Central	odds ratio for health-care seeking (adults) if region is Central	Real	0.6
odds_ratio_adults_region_Southern	odds ratio for health-care seeking (adults) if region is Southern	Real	0.68
odds_ratio_adults_wealth_higher	odds ratio for health-care seeking (adults) if wealth is in categories 4 or 5	Real	1.56
max_days_delay_to_generic_HSI_after_symptoms	Maximum days delay between symptom onset and firstgeneric HSI. Actual delay is sample between 0 and this value.	Integer	4

HealthSystem

Name	Description	Type	Value
Master_Facilities_List	Listing of all health facilities.	Dataframe	…
Officer_Types_Table	The names of the types of health workers (“officers”)	Dataframe	…
Appt_Types_Table	The names of the type of appointments with the health system	Dataframe	…
Appt_Offered_By_Facility_Level	Table indicating whether or not each appointment is offered at each facility level.	Dataframe	…
Appt_Time_Table	The time taken for each appointment, according to officer and facility type.	Dataframe	…
Daily_Capabilities_actual	The capabilities (minutes of time available of each type of officer in each facility) based on the _estimated current_ number and distribution of staff estimated.	Dataframe	…
Daily_Capabilities_funded	The capabilities (minutes of time available of each type of officer in each facility) based on the _potential_ number and distribution of staff estimated (i.e. those positions that can be funded).	Dataframe	…
Daily_Capabilities_funded_plus	The capabilities (minutes of time available of each type of officer in each facility) based on the _potential_ number and distribution of staff estimated, with adjustments to permit each appointment type that should be run at facility level to do so in every district.	Dataframe	…
use_funded_or_actual_staffing	If actual, then use the numbers and distribution of staff estimated to be available currently; If funded, then use the numbers and distribution of staff that are potentially available. If funded_plus, then use a dataset in which the allocation of staff to facilities is tweaked so as to allow each appointment type to run at each facility_level in each district for which it is defined. N.B. This parameter is over-ridden if an argument is provided to the module initialiser.	String	actual
item_and_package_code_lookups	Data imported from the OneHealth Tool on consumable items, packages and costs.	Dataframe	…
consumables_item_designations	Look-up table for the designations of consumables (whether diagnostic, medicine, or other	Dataframe	…
availability_estimates	Estimated availability of consumables in the LMIS dataset.	Dataframe	…
cons_availability	Availability of consumables. If ‘default’ then use the availability specified in the ResourceFile; if ‘none’, then let no consumable be ever be available; if ‘all’, then all consumables are always available. When using ‘all’ or ‘none’, requests for consumables are not logged. NB. This parameter is over-riddenif an argument is provided to the module initialiser.Note that other options are also available: see the Consumables class.	String	default
BedCapacity	Data on the number of beds available of each type by facility_id	Dataframe	…
beds_availability	Availability of beds. If ‘default’ then use the availability specified in the ResourceFile; if ‘none’, then let no beds be ever be available; if ‘all’, then all beds are always available. NB. This parameter is over-ridden if an argument is provided to the module initialiser.	String	default
EquipmentCatalogue	Data on equipment items and packages.	Dataframe	…
equipment_availability_estimates	Data on the availability of equipment items and packages.	Dataframe	…
equip_availability	What to assume about the availability of equipment. If ‘default’ then use the availability specified in the ResourceFile; if ‘none’, then let no equipment ever be available; if ‘all’, then all equipment is always available. NB. This parameter is over-ridden if an argument is provided to the module initialiser.	String	all
equip_availability_postSwitch	What to assume about the availability of equipment after the switch (see year_equip_availability_switch). The options for this are the same as equip_availability.	String	default
year_equip_availability_switch	Year in which the assumption for equip_availability changes (The change happens on 1st January of that year.)	Integer	2100
Service_Availability	List of services to be available. NB. This parameter is over-ridden if an argument is provided to the module initialiser.	List	[‘*’]
policy_name	Name of priority policy adopted	String	Naive
year_mode_switch	Year in which mode switch is enforced	Integer	2100
scale_to_effective_capabilities	In year in which mode switch takes place, will rescale available capabilities to match thosethat were effectively used (on average) in the past year if this is set to True. This way,we can approximate overtime and rushing of appts even in mode 2.	Boolean	False
year_cons_availability_switch	Year in which consumable availability switch is enforced. The change happenson 1st January of that year.)	Integer	2100
year_use_funded_or_actual_staffing_switch	Year in which switch for use_funded_or_actual_staffing is enforced. (The change happenson 1st January of that year.)	Integer	2100
priority_rank	Data on the priority ranking of each of the Treatment_IDs to be adopted by the queueing system under different policies, where the lower the number the higher the priority, and on which categories of individuals classify for fast-tracking for specific treatments	Dictionary	…
HR_scaling_by_level_and_officer_type_table	Factors by which capabilities of medical officer types at different levels will bescaled at the start of the year specified by year_HR_scaling_by_level_and_officer_type. Thisserves to simulate a number of effects (e.g. absenteeism, boosting capabilities of specific medical cadres, etc). This is the imported from an Excel workbook: keys are the worksheet names and values are the worksheets in the format of pd.DataFrames. Additional scenarios can be added by adding worksheets to this workbook: the value of HR_scaling_by_level_and_officer_type_mode indicates which sheet is used.	Dictionary	…
year_HR_scaling_by_level_and_officer_type	Year in which one-off constant HR scaling will take place. (The change happenson 1st January of that year.)	Integer	2100
HR_scaling_by_level_and_officer_type_mode	Mode of HR scaling considered at the start of the simulation. This corresponds to the nameof the worksheet in ResourceFile_HR_scaling_by_level_and_officer_type.xlsx that should be used. Options are: default (capabilities are scaled by a constaint factor of 1); data (factors informed by survey data); and, custom (user can freely set these factors as parameters in the analysis).	String	default
HR_scaling_by_district_table	Factors by which daily capabilities in different districts will bescaled at the start of the year specified by year_HR_scaling_by_district to simulate(e.g., through catastrophic event disrupting delivery of services in particular district(s)).This is the import of an Excel workbook: keys are the worksheet names and values are the worksheets in the format of pd.DataFrames. Additional scenarios can be added by adding worksheets to this workbook: the value of HR_scaling_by_district_mode indicates whichsheet is used.	Dictionary	…
year_HR_scaling_by_district	Year in which scaling of daily capabilities by district will take place. (The change happenson 1st January of that year.)	Integer	2100
HR_scaling_by_district_mode	Mode of scaling of daily capabilities by district. This corresponds to the name of the worksheet in the file ResourceFile_HR_scaling_by_district.xlsx.	String	default
yearly_HR_scaling	Factors by which HR capabilities are scaled. Each sheet specifies a ‘mode’ for dynamic HR scaling. The mode to use is determined by the parameter yearly_HR_scaling_mode. Each sheet must have the same format, including the same column headers. On each sheet, the first row (for 2010, when the simulation starts) specifies the initial configuration: dynamic_HR_scaling_factor (float) is the factor by which all human resoucres capabilities and multiplied; scale_HR_by_popsize (bool) specifies whether the capabilities should (also) grow by the factor by which the population has grown in the last year. Each subsequent row specifies a year where there should be a CHANGE in the configuration. If there are no further rows, then there is no change. But, for example, an additional row of the form `2015, 1.05, TRUE` would mean that on 1st January of 2015, 2016, 2017, ….(and the rest of the simulation), the capabilities would increase by the product of 1.05 and by the ratio of the population size to that in the year previous.	Dictionary	…
yearly_HR_scaling_mode	Specifies which of the policies in yearly_HR_scaling should be adopted. This corresponds toa worksheet of the file ResourceFile_dynamic_HR_scaling.xlsx.	String	no_scaling
tclose_overwrite	Decide whether to overwrite tclose variables assigned by disease modules	Integer	0
tclose_days_offset_overwrite	Offset in days from topen at which tclose will be set by the healthsystem for all HSIsif tclose_overwrite is set to True.	Integer	7
mode_appt_constraints	Integer code in {0, 1, 2} determining mode of constraints with regards to officer numbers and time - 0: no constraints, all HSI events run with no squeeze factor, 1: elastic constraints, all HSI events run with squeeze factor, 2: hard constraints, only HSI events with no squeeze factor run. N.B. This parameter is over-ridden if an argument is provided to the module initialiser.	Integer	1
mode_appt_constraints_postSwitch	Mode considered after a mode switch in year_mode_switch.	Integer	1
cons_availability_postSwitch	Consumables availability after switch in year_cons_availability_switch. Acceptable valuesare the same as those for Parameter cons_availability.	String	default
use_funded_or_actual_staffing_postSwitch	Staffing availability after switch in year_use_funded_or_actual_staffing_switch. Acceptable values are the same as those for Parameter use_funded_or_actual_staffing.	String	funded_plus

Master_Facilities_List

District	Facility_Level	Region	Facility_ID	Facility_Name
Balaka	1a	Southern	1	Facility_Level_1a_Balaka
Balaka	1b	Southern	2	Facility_Level_1b_Balaka
Balaka	2	Southern	3	Facility_Level_2_Balaka
Blantyre	0	Southern	4	Facility_Level_0_Blantyre
Blantyre	1a	Southern	5	Facility_Level_1a_Blantyre
Blantyre	1b	Southern	6	Facility_Level_1b_Blantyre
Blantyre	2	Southern	7	Facility_Level_2_Blantyre
Blantyre City	0	Southern	8	Facility_Level_0_Blantyre City
Blantyre City	1a	Southern	9	Facility_Level_1a_Blantyre City

Only first 10 rows of 133 are shown.

Officer_Types_Table

Officer_Type	Officer_Type_Code	Officer_Category
Clinical Officer / Technician	M02	Clinical
Med. Assistant	M03	Clinical
Nurse Officer	N01	Nursing_and_Midwifery
Nurse Midwife Technician	N02	Nursing_and_Midwifery
Pharmacist	P01	Pharmacy
Pharm Technician	P02	Pharmacy
Pharm Assistant	P03	Pharmacy
Lab Officer	L01	Laboratory
Lab Technician	L02	Laboratory

Only first 10 rows of 21 are shown.

Appt_Types_Table

Appt_Type_Code	Appt_Cat	Appt_Type
IPAdmission	GENERAL_INPATIENT_AND_OUTPATIENT_CARE	Inpatient Admissions and Discharge Process
Under5OPD	GENERAL_INPATIENT_AND_OUTPATIENT_CARE	Under 5 Outpatient Visit
Over5OPD	GENERAL_INPATIENT_AND_OUTPATIENT_CARE	Over 5 Outpatient visit
NormalDelivery	RMNCH	Normal Deliveries
CompDelivery	RMNCH	Complicated Deliveries
Csection	RMNCH	Caesarean Sections
FamPlan	RMNCH	Family Planning
AntenatalFirst	RMNCH	Antenatal Care - First Visit
ANCSubsequent	RMNCH	Antenatal Care - Followup Visit

Only first 10 rows of 50 are shown.

Appt_Offered_By_Facility_Level

Appt_Type_Code	Facility_Level_0	Facility_Level_1a	Facility_Level_1b	Facility_Level_2	Facility_Level_3	Facility_Level_4	Facility_Level_5
IPAdmission	False	True	True	True	True	False	False
Under5OPD	False	True	True	True	True	False	False
Over5OPD	False	True	True	True	True	False	False
NormalDelivery	False	True	True	True	True	False	False
CompDelivery	False	True	True	True	True	False	False
Csection	False	True	True	True	True	False	False
FamPlan	False	True	True	True	False	False	False
AntenatalFirst	False	True	True	True	True	False	False
ANCSubsequent	False	True	True	True	True	False	False

Only first 10 rows of 50 are shown.

Appt_Time_Table

Appt_Type_Code	Facility_Level	Officer_Category	Time_Taken_Mins
ANCSubsequent	2	Nursing_and_Midwifery	18
ANCSubsequent	2	Pharmacy	1
ANCSubsequent	3	Clinical	3
ANCSubsequent	3	Nursing_and_Midwifery	15
ANCSubsequent	3	Pharmacy	5
ANCSubsequent	1a	Clinical	1
ANCSubsequent	1a	Nursing_and_Midwifery	11
ANCSubsequent	1a	Pharmacy	0.4
ANCSubsequent	1b	Clinical	2

Only first 10 rows of 345 are shown.

Daily_Capabilities_actual

Facility_ID	Facility_Name	Facility_Level	District	Region	Officer_Category	Total_Mins_Per_Day	Staff_Count
0	Facility_Level_0_Balaka	0	Balaka	Southern	DCSA	17362.5	311
0	Facility_Level_0_Balaka	0	Balaka	Southern	Dental	0	0
0	Facility_Level_0_Balaka	0	Balaka	Southern	Laboratory	0	0
0	Facility_Level_0_Balaka	0	Balaka	Southern	Mental	0	0
0	Facility_Level_0_Balaka	0	Balaka	Southern	Nursing_and_Midwifery	0	0
0	Facility_Level_0_Balaka	0	Balaka	Southern	Nutrition	0	0
0	Facility_Level_0_Balaka	0	Balaka	Southern	Pharmacy	0	0
0	Facility_Level_0_Balaka	0	Balaka	Southern	Radiography	0	0
1	Facility_Level_1a_Balaka	1a	Balaka	Southern	Clinical	7764.57	35.9682

Only first 10 rows of 1197 are shown.

Daily_Capabilities_funded

Facility_ID	Facility_Name	Facility_Level	District	Region	Officer_Category	Total_Mins_Per_Day	Staff_Count
0	Facility_Level_0_Balaka	0	Balaka	Southern	DCSA	13957	250
0	Facility_Level_0_Balaka	0	Balaka	Southern	Dental	0	0
0	Facility_Level_0_Balaka	0	Balaka	Southern	Laboratory	0	0
0	Facility_Level_0_Balaka	0	Balaka	Southern	Mental	0	0
0	Facility_Level_0_Balaka	0	Balaka	Southern	Nursing_and_Midwifery	0	0
0	Facility_Level_0_Balaka	0	Balaka	Southern	Nutrition	0	0
0	Facility_Level_0_Balaka	0	Balaka	Southern	Pharmacy	0	0
0	Facility_Level_0_Balaka	0	Balaka	Southern	Radiography	0	0
1	Facility_Level_1a_Balaka	1a	Balaka	Southern	Clinical	9786.98	47.0287

Only first 10 rows of 1197 are shown.

Daily_Capabilities_funded_plus

Facility_ID	Facility_Name	Facility_Level	District	Region	Officer_Category	Total_Mins_Per_Day	Staff_Count
1	Facility_Level_1a_Balaka	1a	Balaka	Southern	Clinical	9786.98	47.0287
1	Facility_Level_1a_Balaka	1a	Balaka	Southern	Dental	2327.32	11.3933
1	Facility_Level_1a_Balaka	1a	Balaka	Southern	Laboratory	5012.02	24.9123
1	Facility_Level_1a_Balaka	1a	Balaka	Southern	Nursing_and_Midwifery	31874.9	150.48
1	Facility_Level_1a_Balaka	1a	Balaka	Southern	Nutrition	110.791	0.542373
1	Facility_Level_1a_Balaka	1a	Balaka	Southern	Pharmacy	4132.1	20.6361
2	Facility_Level_1b_Balaka	1b	Balaka	Southern	Clinical	6470	31.8781
2	Facility_Level_1b_Balaka	1b	Balaka	Southern	Dental	719.736	3.52345
2	Facility_Level_1b_Balaka	1b	Balaka	Southern	Laboratory	1340.35	5.95697

Only first 10 rows of 733 are shown.

item_and_package_code_lookups

Intervention_Cat	Intervention_Pkg	Intervention_Pkg_Code	Items	Item_Code	Expected_Units_Per_Case	Unit_Cost
Maternal/Newborn and Reproductive Health	Pill	0	Levonorgestrel 0.15 mg + Ethinyl estradiol 30 mcg (Microgynon), cycle	1	7.5	53.3501
Maternal/Newborn and Reproductive Health	Male condom	1	Condom, male	2	120	20.9702
Maternal/Newborn and Reproductive Health	Injectable	2	Depot-Medroxyprogesterone Acetate 150 mg - 3 monthly	3	4	50.9439
Maternal/Newborn and Reproductive Health	Injectable	2	Gloves, exam, latex, disposable, pair	4	4	31.9087
Maternal/Newborn and Reproductive Health	Injectable	2	Povidone iodine, solution, 10 %, 5 ml per injection	5	4	2.00634
Maternal/Newborn and Reproductive Health	Injectable	2	Syringe, Autodisable SoloShot IX	6	4	5.4264
Maternal/Newborn and Reproductive Health	IUD	3	Gloves, exam, latex, disposable, pair	4	3	31.9087
Maternal/Newborn and Reproductive Health	IUD	3	IUD, Copper T-380A	7	1	19.3922
Maternal/Newborn and Reproductive Health	Implant	4	Gloves, exam, latex, disposable, pair	4	2	31.9087

Only first 10 rows of 2444 are shown.

consumables_item_designations

is_diagnostic	is_medicine	is_other	is_vital	is_drug_or_vaccine
0	0	1	1	0
0	1	0	1	1
0	0	1	1	0
0	1	0	1	0
0	0	1	1	0
0	1	0	1	0
0	1	0	0	1
0	0	1	1	0
0	0	1	1	0

Only first 10 rows of 2016 are shown.

availability_estimates

Facility_ID	month	item_code	available_prop
0	1	1	0.3825
0	1	2	0.555
0	1	3	0.33875
0	1	5	0.145161
0	1	6	0.609167
0	1	7	0.4
0	1	8	0
0	1	11	0.25
0	1	12	0.357143

Only first 10 rows of 307296 are shown.

BedCapacity

Facility_ID	maternity_bed	delivery_bed	general_bed	non_bed_space
1	134	29	14	1000
2	49	6	57	1000
3	35	4	54	1000
4	0	0	0	0
5	168	32	50	1000
6	61	7	195	1000
7	44	4	184	1000
8	0	0	0	0
9	168	32	50	1000

Only first 10 rows of 133 are shown.

EquipmentCatalogue

Item_Description	Item_Code	Pkg_Name	Source_Equip_Item	Alternative item names
Weighing scale	1	ANC	Malawi HSSPIII Equipment Costing 2023	‘Salter weighing scale’, ‘Waeighing Scale’
Autoclave	2	nan	Malawi HSSPIII Equipment Costing 2023	‘High pressure cooker sterilizer, complete with stove’, ‘Sterilization drums, medium’, ‘Sterilization drum’, ‘Sterilization buckets’, ‘Sterilization buckets (decontamination buckets)’, ‘Sterilization Buckets’, ‘Decontamination drums’, ‘Dressing drum medium’, ‘Dressing drum large’, ‘Dressing drum small’
Refrigerator	3	nan	Malawi HSSPIII Equipment Costing 2023	‘Vaccine refrigerator (solar)’, ‘Vaccine Refrigerator’
Cold box	4	nan	Malawi HSSPIII Equipment Costing 2023	‘Cold Chain Box-large’, ‘Cold Chain Box-medium’
Vaccine Carriers	5	nan	Malawi HSSPIII Equipment Costing 2023	nan
Blood pressure machine	6	Minor Surgery, Major Surgery, ICU	Malawi HSSPIII Equipment Costing 2023	nan
Thermometer	7	nan	Malawi HSSPIII Equipment Costing 2023	‘Thermometers, digital’
Push bike for mobility	8	nan	Malawi HSSPIII Equipment Costing 2023	nan
Desk	9	nan	Malawi HSSPIII Equipment Costing 2023	‘Office desk’

Only first 10 rows of 404 are shown.

equipment_availability_estimates

Facility_ID	Item_Code	Pr_Available
0	1	0.75
0	2	1
0	3	1
0	4	0.226281
0	5	0.226281
0	6	0.25
0	7	0.75
0	8	0.226281
0	9	0.226281

Only first 10 rows of 53732 are shown.

priority_rank

Default

Treatment	Priority	FT_if_5orUnder	FT_if_pregnant	FT_if_tbdiagnosed	FT_if_Hivdiagnosed
FirstAttendance_SpuriousEmergencyCare	0	-1	-1	-1	-1
Alri_Pneumonia_Treatment_Outpatient	0	-1	-1	-1	-1
Alri_Pneumonia_Treatment_Inpatient	0	-1	-1	-1	-1
Alri_Pneumonia_Treatment_Inpatient_Followup	0	-1	-1	-1	-1
BladderCancer_Investigation	0	-1	-1	-1	-1
BladderCancer_PalliativeCare	0	-1	-1	-1	-1
BladderCancer_Treatment	0	-1	-1	-1	-1
BreastCancer_Investigation	0	-1	-1	-1	-1
BreastCancer_PalliativeCare	0	-1	-1	-1	-1

Only first 10 rows of 87 are shown.

Test

Treatment	Priority	FT_if_5orUnder	FT_if_pregnant	FT_if_tbdiagnosed	FT_if_Hivdiagnosed
FirstAttendance_SpuriousEmergencyCare	0	-1	-1	-1	-1
Alri_Pneumonia_Treatment_Outpatient	0	-1	-1	-1	-1
Alri_Pneumonia_Treatment_Inpatient	0	-1	-1	-1	-1
Alri_Pneumonia_Treatment_Inpatient_Followup	0	-1	-1	-1	-1
BladderCancer_Investigation	0	-1	-1	-1	-1
BladderCancer_PalliativeCare	0	-1	-1	-1	-1
BladderCancer_Treatment	0	-1	-1	-1	-1
BreastCancer_Investigation	0	-1	-1	-1	-1
BreastCancer_PalliativeCare	0	-1	-1	-1	-1

Only first 10 rows of 87 are shown.

Naive

Treatment	Priority	FT_if_5orUnder	FT_if_pregnant	FT_if_tbdiagnosed	FT_if_Hivdiagnosed
FirstAttendance_SpuriousEmergencyCare	1	0	-1	-1	-1
Alri_Pneumonia_Treatment_Outpatient	2	-1	-1	-1	-1
Alri_Pneumonia_Treatment_Inpatient	2	-1	-1	-1	-1
Alri_Pneumonia_Treatment_Inpatient_Followup	2	-1	-1	-1	-1
BladderCancer_Investigation	2	-1	-1	-1	-1
BladderCancer_PalliativeCare	2	-1	-1	-1	-1
BladderCancer_Treatment	2	-1	-1	-1	-1
BreastCancer_Investigation	2	-1	-1	-1	-1
BreastCancer_PalliativeCare	2	-1	-1	-1	-1

Only first 10 rows of 87 are shown.

Test Mode 1

Treatment	Priority	FT_if_5orUnder	FT_if_pregnant	FT_if_tbdiagnosed	FT_if_Hivdiagnosed
FirstAttendance_SpuriousEmergencyCare	4	-1	-1	-1	-1
Alri_Pneumonia_Treatment_Outpatient	0	-1	-1	-1	-1
Alri_Pneumonia_Treatment_Inpatient	4	-1	-1	-1	-1
Alri_Pneumonia_Treatment_Inpatient_Followup	0	-1	-1	-1	-1
BladderCancer_Investigation	4	-1	-1	-1	-1
BladderCancer_PalliativeCare	0	-1	-1	-1	-1
BladderCancer_Treatment	4	-1	-1	-1	-1
BreastCancer_Investigation	0	-1	-1	-1	-1
BreastCancer_PalliativeCare	4	-1	-1	-1	-1

Only first 10 rows of 87 are shown.

ClinicallyVulnerable

Treatment	Priority	FT_if_5orUnder	FT_if_pregnant	FT_if_tbdiagnosed	FT_if_Hivdiagnosed
FirstAttendance_SpuriousEmergencyCare	1	0	-1	-1	-1
Alri_Pneumonia_Treatment_Outpatient	3	2	2	2	2
Alri_Pneumonia_Treatment_Inpatient	3	2	2	2	2
Alri_Pneumonia_Treatment_Inpatient_Followup	3	2	2	2	2
BladderCancer_Investigation	3	2	2	2	2
BladderCancer_PalliativeCare	3	2	2	2	2
BladderCancer_Treatment	3	2	2	2	2
BreastCancer_Investigation	3	2	2	2	2
BreastCancer_PalliativeCare	3	2	2	2	2

Only first 10 rows of 87 are shown.

VerticalProgrammes

Treatment	Priority	FT_if_5orUnder	FT_if_pregnant	FT_if_tbdiagnosed	FT_if_Hivdiagnosed
FirstAttendance_SpuriousEmergencyCare	1	0	-1	-1	-1
Alri_Pneumonia_Treatment_Outpatient	3	-1	-1	-1	-1
Alri_Pneumonia_Treatment_Inpatient	3	-1	-1	-1	-1
Alri_Pneumonia_Treatment_Inpatient_Followup	3	-1	-1	-1	-1
BladderCancer_Investigation	3	-1	-1	-1	-1
BladderCancer_PalliativeCare	3	-1	-1	-1	-1
BladderCancer_Treatment	3	-1	-1	-1	-1
BreastCancer_Investigation	3	-1	-1	-1	-1
BreastCancer_PalliativeCare	3	-1	-1	-1	-1

Only first 10 rows of 87 are shown.

RMNCH

Treatment	Priority	FT_if_5orUnder	FT_if_pregnant	FT_if_tbdiagnosed	FT_if_Hivdiagnosed
FirstAttendance_SpuriousEmergencyCare	1	0	-1	-1	-1
Alri_Pneumonia_Treatment_Outpatient	5	3	-1	-1	-1
Alri_Pneumonia_Treatment_Inpatient	5	3	-1	-1	-1
Alri_Pneumonia_Treatment_Inpatient_Followup	5	3	-1	-1	-1
BladderCancer_Investigation	5	-1	-1	-1	-1
BladderCancer_PalliativeCare	5	-1	-1	-1	-1
BladderCancer_Treatment	5	-1	-1	-1	-1
BreastCancer_Investigation	5	-1	-1	-1	-1
BreastCancer_PalliativeCare	5	-1	-1	-1	-1

Only first 10 rows of 87 are shown.

EHP_III

Treatment	Priority	FT_if_5orUnder	FT_if_pregnant	FT_if_tbdiagnosed	FT_if_Hivdiagnosed
FirstAttendance_SpuriousEmergencyCare	1	0	-1	-1	-1
Alri_Pneumonia_Treatment_Outpatient	2	-1	-1	-1	-1
Alri_Pneumonia_Treatment_Inpatient	2	-1	-1	-1	-1
Alri_Pneumonia_Treatment_Inpatient_Followup	2	-1	-1	-1	-1
BladderCancer_Investigation	4	-1	-1	-1	-1
BladderCancer_PalliativeCare	4	-1	-1	-1	-1
BladderCancer_Treatment	4	-1	-1	-1	-1
BreastCancer_Investigation	4	-1	-1	-1	-1
BreastCancer_PalliativeCare	4	-1	-1	-1	-1

Only first 10 rows of 87 are shown.

LCOA_EHP

Treatment	Priority	FT_if_5orUnder	FT_if_pregnant	FT_if_tbdiagnosed	FT_if_Hivdiagnosed
FirstAttendance_SpuriousEmergencyCare	1	0	-1	-1	-1
Alri_Pneumonia_Treatment_Outpatient	2	-1	-1	-1	-1
Alri_Pneumonia_Treatment_Inpatient	3	-1	-1	-1	-1
Alri_Pneumonia_Treatment_Inpatient_Followup	3	-1	-1	-1	-1
BladderCancer_Investigation	4	-1	-1	-1	-1
BladderCancer_PalliativeCare	4	-1	-1	-1	-1
BladderCancer_Treatment	4	-1	-1	-1	-1
BreastCancer_Investigation	4	-1	-1	-1	-1
BreastCancer_PalliativeCare	4	-1	-1	-1	-1

Only first 10 rows of 87 are shown.

CVD

Treatment	Priority	FT_if_5orUnder	FT_if_pregnant	FT_if_tbdiagnosed	FT_if_Hivdiagnosed
FirstAttendance_SpuriousEmergencyCare	1	0	-1	-1	-1
Alri_Pneumonia_Treatment_Outpatient	3	-1	-1	-1	-1
Alri_Pneumonia_Treatment_Inpatient	3	-1	-1	-1	-1
Alri_Pneumonia_Treatment_Inpatient_Followup	3	-1	-1	-1	-1
BladderCancer_Investigation	3	-1	-1	-1	-1
BladderCancer_PalliativeCare	3	-1	-1	-1	-1
BladderCancer_Treatment	3	-1	-1	-1	-1
BreastCancer_Investigation	3	-1	-1	-1	-1
BreastCancer_PalliativeCare	3	-1	-1	-1	-1

Only first 10 rows of 87 are shown.

HR_scaling_by_level_and_officer_type_table

default

Officer_Category	L0_factor	L1a_factor	L1b_factor	L2_factor	L3_factor	L4_factor	L5_factor
Clinical	1	1	1	1	1	1	1
DCSA	1	1	1	1	1	1	1
Dental	1	1	1	1	1	1	1
Laboratory	1	1	1	1	1	1	1
Mental	1	1	1	1	1	1	1
Nursing_and_Midwifery	1	1	1	1	1	1	1
Nutrition	1	1	1	1	1	1	1
Pharmacy	1	1	1	1	1	1	1
Radiography	1	1	1	1	1	1	1

data

Officer_Category	L0_factor	L1a_factor	L1b_factor	L2_factor	L3_factor	L4_factor	L5_factor
Clinical	1	0.795927	0.836783	1.00678	1	1	1
DCSA	2.13327	1	1	1	1	1	1
Dental	1	1.46777	1.46777	1.46777	1	1	1
Laboratory	1	1.0149	0.997807	1.14721	1	1	1
Mental	1	1	1	1	1	1	1
Nursing_and_Midwifery	1	0.605695	0.615689	0.799333	1	1	1
Nutrition	1	1	1	1	1	1	1
Pharmacy	1	1.02347	1.06089	1.30115	1	1	1
Radiography	1	1	0.275236	0.277971	1	1	1

custom

Officer_Category	L0_factor	L1a_factor	L1b_factor	L2_factor	L3_factor	L4_factor	L5_factor
Clinical	0.5	0.5	0.5	0.5	0.5	0.5	0.5
DCSA	0.5	0.5	0.5	0.5	0.5	0.5	0.5
Dental	0.5	0.5	0.5	0.5	0.5	0.5	0.5
Laboratory	0.5	0.5	0.5	0.5	0.5	0.5	0.5
Mental	0.5	0.5	0.5	0.5	0.5	0.5	0.5
Nursing_and_Midwifery	0.5	0.5	0.5	0.5	0.5	0.5	0.5
Nutrition	0.5	0.5	0.5	0.5	0.5	0.5	0.5
Pharmacy	0.5	0.5	0.5	0.5	0.5	0.5	0.5
Radiography	0.5	0.5	0.5	0.5	0.5	0.5	0.5

x2_fac0&1

Officer_Category	L0_factor	L1a_factor	L1b_factor	L2_factor	L3_factor	L4_factor	L5_factor
Clinical	2	2	2	1	1	1	1
DCSA	2	2	2	1	1	1	1
Dental	2	2	2	1	1	1	1
Laboratory	2	2	2	1	1	1	1
Mental	2	2	2	1	1	1	1
Nursing_and_Midwifery	2	2	2	1	1	1	1
Nutrition	2	2	2	1	1	1	1
Pharmacy	2	2	2	1	1	1	1
Radiography	2	2	2	1	1	1	1

HR_scaling_by_district_table

default

District	Factor
Blantyre	1
Blantyre City	1
Chikwawa	1
Chiradzulu	1
Chitipa	1
Dedza	1
Dowa	1
Karonga	1
Kasungu	1

Only first 10 rows of 32 are shown.

yearly_HR_scaling

no_scaling

year	dynamic_HR_scaling_factor	scale_HR_by_popsize
2010	1	False

scaling_by_population_growth

year	dynamic_HR_scaling_factor	scale_HR_by_popsize
2010	1	False
2019	1	True

GDP_growth

year	dynamic_HR_scaling_factor	scale_HR_by_popsize
2010	1	False
2019	1.042	False

GDP_growth_fHE_case1

year	dynamic_HR_scaling_factor	scale_HR_by_popsize
2010	1	False
2019	1.01074	False

GDP_growth_fHE_case2

year	dynamic_HR_scaling_factor	scale_HR_by_popsize
2010	1	False
2019	1.02116	False

GDP_growth_fHE_case3

year	dynamic_HR_scaling_factor	scale_HR_by_popsize
2010	1	False
2019	1.02637	False

GDP_growth_fHE_case4

year	dynamic_HR_scaling_factor	scale_HR_by_popsize
2010	1	False
2019	1.05763	False

GDP_growth_fHE_case5

year	dynamic_HR_scaling_factor	scale_HR_by_popsize
2010	1	False
2019	1.06284	False

GDP_growth_fHE_case6

year	dynamic_HR_scaling_factor	scale_HR_by_popsize
2010	1	False
2019	1.07326	False

GDP_growth_FL_case1_const_tot_i

year	dynamic_HR_scaling_factor	scale_HR_by_popsize
2010	1	False
2018	1.1	False
2019	1.042	False
2032	0.861157	False
2033	1.042	False

GDP_growth_FL_case2_const_tot_i

year	dynamic_HR_scaling_factor	scale_HR_by_popsize
2010	1	False
2018	1.3	False
2019	1.042	False
2031	0.616568	False
2032	1.042	False

GDP_growth_FL_case1_vary_tot_in

year	dynamic_HR_scaling_factor	scale_HR_by_popsize
2010	1	False
2018	1.1	False
2019	1.042	False

GDP_growth_FL_case2_vary_tot_in

year	dynamic_HR_scaling_factor	scale_HR_by_popsize
2010	1	False
2018	1.3	False
2019	1.042	False

Hiv

Name	Description	Type	Value
time_inf	prob of time since infection for baseline adult pop	Dataframe	…
art_coverage	coverage of ART at baseline	Dataframe	…
treatment_cascade	spectrum estimates of treatment cascade	Dataframe	…
beta	Transmission rate	Real	0.14379
unaids_prevalence_adjustment_factor	adjustment for baseline age-specific prevalence values to give correct population prevalence	Real	1.1
prob_mtct_untreated	Probability of mother to child transmission	Real	0.22
prob_mtct_treated	Probability of mother to child transmission, mother on ART	Real	0.0
prob_mtct_incident_preg	Probability of mother to child transmission, mother infected during pregnancy	Real	0.3
monthly_prob_mtct_bf_untreated	Probability of mother to child transmission during breastfeeding	Real	0.01
monthly_prob_mtct_bf_treated	Probability of mother to child transmission, mother infected during breastfeeding	Real	0.0
rr_fsw	Relative risk of HIV with female sex work	Real	25.0
rr_circumcision	Relative risk of HIV with circumcision	Real	0.4
rr_rural	Relative risk of HIV in rural location	Real	0.52
rr_windex_poorer	Relative risk of HIV with wealth level poorer	Real	0.96
rr_windex_middle	Relative risk of HIV with wealth level middle	Real	1.18
rr_windex_richer	Relative risk of HIV with wealth level richer	Real	1.19
rr_windex_richest	Relative risk of HIV with wealth level richest	Real	1.56
rr_sex_f	Relative risk of HIV if female	Real	1.43
rr_edlevel_primary	Relative risk of HIV with primary education	Real	1.18
rr_edlevel_secondary	Relative risk of HIV with secondary education	Real	1.15
rr_edlevel_higher	Relative risk of HIV with higher education	Real	1.0
rr_schisto	Relative risk of HIV with high intensity S. haematobium infection	Real	2.3
rr_behaviour_change	Relative risk of HIV with behaviour modification	Real	0.75
proportion_reduction_in_risk_of_hiv_aq_if_on_prep	Proportion reduction in risk of HIV acquisition if on PrEP. 0 for no efficacy; 1.0 for perfect efficacy.	Real	0.9
mean_months_between_aids_and_death	Mean number of months (distributed exponentially) for the time between AIDS and AIDS Death	Real	18.0
mean_months_between_aids_and_death_infant	Mean number of months for the time between AIDS and AIDS Death for infants	Real	6.0
infection_to_death_weibull_shape_1519	Shape parameter for Weibull describing time between infection and death for 15-19 yo (units: years)	Real	2.0
infection_to_death_weibull_shape_2024	Shape parameter for Weibull describing time between infection and death for 20-24 yo (units: years)	Real	2.0
infection_to_death_weibull_shape_2529	Shape parameter for Weibull describing time between infection and death for 25-29 yo (units: years)	Real	2.0
infection_to_death_weibull_shape_3034	Shape parameter for Weibull describing time between infection and death for 30-34 yo (units: years)	Real	2.0
infection_to_death_weibull_shape_3539	Shape parameter for Weibull describing time between infection and death for 35-39 yo (units: years)	Real	2.0
infection_to_death_weibull_shape_4044	Shape parameter for Weibull describing time between infection and death for 40-44 yo (units: years)	Real	2.0
infection_to_death_weibull_shape_4549	Shape parameter for Weibull describing time between infection and death for 45-49 yo (units: years)	Real	2.0
infection_to_death_weibull_scale_1519	Scale parameter for Weibull describing time between infection and death for 15-19 yo (units: years)	Real	16.0
infection_to_death_weibull_scale_2024	Scale parameter for Weibull describing time between infection and death for 20-24 yo (units: years)	Real	15.4
infection_to_death_weibull_scale_2529	Scale parameter for Weibull describing time between infection and death for 25-29 yo (units: years)	Real	14.1
infection_to_death_weibull_scale_3034	Scale parameter for Weibull describing time between infection and death for 30-34 yo (units: years)	Real	12.1
infection_to_death_weibull_scale_3539	Scale parameter for Weibull describing time between infection and death for 35-39 yo (units: years)	Real	11.0
infection_to_death_weibull_scale_4044	Scale parameter for Weibull describing time between infection and death for 40-44 yo (units: years)	Real	10.01
infection_to_death_weibull_scale_4549	Scale parameter for Weibull describing time between infection and death for 45-49 yo (units: years)	Real	7.9
art_default_to_aids_mean_years	Mean years between when a person (any change) stops being on treatment to when AIDS is onset (if the absence of resuming treatment).	Real	5.0
prop_delayed_aids_onset	Proportion of PLHIV that will have delayed AIDS onset to compensate for AIDS-TB	Real	0.3
mean_survival_for_infants_infected_prior_to_birth	Exponential rate parameter for mortality in infants who are infected before birth	Real	1.08
infection_to_death_infant_infection_after_birth_weibull_scale	Weibull scale parameter for mortality in infants who are infected after birth	Real	16.0
infection_to_death_infant_infection_after_birth_weibull_shape	Weibull shape parameter for mortality in infants who are infected after birth	Real	2.7
hiv_testing_rates	annual rates of testing for children and adults	Dataframe	…
rr_test_hiv_positive	relative likelihood of having HIV test for people with HIV	Real	1.1
hiv_testing_rate_adjustment	adjustment to current testing rates to account for multiple routes into HIV testing	Real	0.75
treatment_initiation_adjustment	adjustment to current ART coverage levels to account for defaulters	Real	1.0
vs_adjustment	adjustment to current viral suppression levels to account for defaulters	Real	1.0
prob_hiv_test_at_anc_or_delivery	probability of a women having hiv test at anc or following delivery	Real	0.95
prob_hiv_test_for_newborn_infant	probability of a newborn infant having HIV test pre-discharge	Real	0.95
prob_start_art_or_vs	Probability that a person will start treatment and be virally suppressed following testing	Dataframe	…
prob_behav_chg_after_hiv_test	Probability that a person will change risk behaviours, if HIV-negative, following testing	Real	0.5
prob_prep_for_fsw_after_hiv_test	Probability that a FSW will start PrEP, if HIV-negative, following testing	Real	0.05
prob_prep_for_agyw	Probability that adolescent girls / young women will start PrEP	Real	0.0
prob_circ_after_hiv_test	Probability that a male will be circumcised, if HIV-negative, following testing	Real	0.05
prob_circ_for_child_before_2020	Probability that a male aging <15 yrs will be circumcised before year 2020	Real	0.0128
prob_circ_for_child_from_2020	Probability that a male aging <15 yrs will be circumcised from year 2020, which is different from before 2020 as children vmmc policy/fund/cases has changed, according to PEPFAR 2020 Country Operational Plan and DHIS2 data	Real	0.0008
probability_of_being_retained_on_prep_every_3_months	Probability that someone who has initiated on prep will attend an appointment and be on prep for the next 3 months, until the next appointment.	Real	0.5
probability_of_being_retained_on_art_every_3_months	Probability that someone who has initiated on treatment will attend an appointment and be on treatment for next 3 months, until the next appointment.	Real	0.95
probability_of_seeking_further_art_appointment_if_drug_not_available	Probability that a person who ‘should’ be on art will seek another appointment (the following day and try for each of the next 7 days) if drugs were not available.	Real	0.9
probability_of_seeking_further_art_appointment_if_appointment_not_available	Probability that a person who ‘should’ be on art will seek another appointment if the health-system has not been able to provide them with an appointment	Real	0.9
prep_start_year	Year from which PrEP is available	Real	2018.0
ART_age_cutoff_young_child	Age cutoff for ART regimen for young children	Integer	1
ART_age_cutoff_older_child	Age cutoff for ART regimen for older children	Integer	10
rel_probability_art_baseline_aids	relative probability of person with HIV infection over 10 years being on ART at baseline	Real	10.0
aids_tb_treatment_adjustment	probability of death if aids and tb, person on treatment for tb	Real	0.5
hiv_healthseekingbehaviour_cap	number of repeat visits assumed for healthcare services	Integer	5
dispensation_period_months	length of prescription for ARVs in months, same for all PLHIV	Real	3.0
length_of_inpatient_stay_if_terminal	length in days of inpatient stay for end-of-life HIV patients: list has two elements [low-bound-inclusive, high-bound-exclusive]	List	[14, 20]
type_of_scaleup	argument to determine type scale-up of program which will be implemented, can be ‘none’, ‘target’ or ‘max’	String	none
scaleup_start_year	the year when the scale-up starts (it will occur on 1st January of that year)	Integer	2025
scaleup_parameters	the parameters and values changed in scenario analysis	Dataframe	…

time_inf

year	probability_infection	scaled_prob	Unnamed: 3	Unnamed: 4	Unnamed: 5	Distribution by CD4 count - HIV+ not on ART (15+) - (Male+Female)	Unnamed: 7	Unnamed: 8	Unnamed: 9	Unnamed: 10	Unnamed: 11	Unnamed: 12	Unnamed: 13	Unnamed: 14	Unnamed: 15	Unnamed: 16
20	0.0145011	0.0167087	nan	nan	nan	malawi_2021_v14_aim_v6.07	nan	nan	nan	nan	nan	nan	nan	nan	nan	nan
19	0.018403	0.0212047	nan	nan	nan	2010	150189.14229	134383.22199	114415.4995	52950.4893	77739.93484	28957.76557	20245.60225	578882	276528	0.350438
18	0.022511	0.0259382	nan	nan	nan	nan	nan	nan	nan	nan	nan	nan	nan	nan	nan	nan
17	0.0264052	0.0304252	nan	nan	nan	Distribution by CD4 count - HIV+ on ART (15+) - (Male+Female)	nan	nan	nan	nan	nan	nan	nan	nan	nan	nan
16	0.0305511	0.0352023	nan	nan	nan	nan	> 500	350 - 500	250 - 349	200 - 249	100 - 199	50 - 99	< 50	nan	nan	nan
15	0.0338398	0.0389916	nan	nan	nan	malawi_2021_v14_aim_v6.07	nan	nan	nan	nan	nan	nan	nan	nan	nan	nan
14	0.0383583	0.044198	nan	nan	nan	2010	6268.17276	5523.92113	4618.85403	44214.79861	77016.22359	36469.29667	36098.98313	210210	nan	nan
13	0.0423454	0.0487921	nan	nan	nan	nan	nan	nan	nan	nan	nan	nan	nan	nan	nan	nan
12	0.0452294	0.0521152	nan	nan	nan	nan	nan	nan	nan	nan	nan	nan	nan	nan	nan	nan

Only first 10 rows of 21 are shown.

art_coverage

year	age	single_age	sex	art_coverage	prop_coverage
2009	0_4	1	F	10.69	0.1069
2009	0_4	2	F	10.69	0.1069
2009	0_4	3	F	10.69	0.1069
2009	0_4	4	F	10.69	0.1069
2009	5_9	5	F	7.6	0.076
2009	5_9	6	F	7.6	0.076
2009	5_9	7	F	7.6	0.076
2009	5_9	8	F	7.6	0.076
2009	5_9	9	F	7.6	0.076

Only first 10 rows of 1662 are shown.

treatment_cascade

year	age	plhiv	know_status	on_art	plhiv_virally_suppressed	prob_art_if_dx	virally_suppressed_on_art	vs_assumed_value
2011	adults	100	73.2277	37.6375	nan	0.513979	80	yes
2012	adults	100	76.423	46.3159	42.1013	0.606046	91	no
2013	adults	100	78.7843	52.9497	47.6735	0.672084	90	no
2014	adults	100	80.8733	59.2378	51.5664	0.732477	87	no
2015	adults	100	82.7952	64.1071	57.269	0.774285	89	no
2016	adults	100	85.3839	71.6873	65.3256	0.839588	91	no
2017	adults	100	88.3281	78.056	69.322	0.883705	89	no
2018	adults	100	90.6581	84.2257	76.8029	0.929047	91	no
2019	adults	100	92.1484	85.4227	79.9867	0.927012	94	no

Only first 10 rows of 32 are shown.

hiv_testing_rates

year	adults_15plus	children0_14	total	pop_size_children0_14	pop_size_adults15plus	annual_testing_rate_children	annual_testing_rate_adults	annual_testing_rate_all_ages	testing_yield
2011	1.47766e+06	147536	1.62766e+06	6.84823e+06	8.2137e+06	0.0215437	0.179902	0.108065	nan
2012	1.54915e+06	149514	1.70682e+06	6.94965e+06	8.51109e+06	0.0215139	0.182016	0.110397	nan
2013	1.56574e+06	136888	1.70263e+06	7.04596e+06	8.8196e+06	0.0194279	0.177529	0.107316	nan
2014	1.73309e+06	161964	1.89506e+06	7.13959e+06	9.13714e+06	0.0226853	0.189676	0.116427	nan
2015	2.01048e+06	215807	2.22629e+06	7.23293e+06	9.46126e+06	0.0298367	0.212496	0.133357	nan
2016	2.91753e+06	483515	3.40104e+06	7.32839e+06	9.79171e+06	0.0659783	0.297959	0.198658	nan
2017	3.62603e+06	539283	4.16531e+06	7.42836e+06	1.01303e+07	0.0725978	0.35794	0.237223	0.023
2018	4.09092e+06	544240	4.63516e+06	7.53526e+06	1.04771e+07	0.0722257	0.390464	0.257332	0.01925
2019	3.64886e+06	418104	4.06697e+06	7.66667e+06	1.09056e+07	0.0545353	0.334586	0.218981	0.01425

Only first 10 rows of 41 are shown.

prob_start_art_or_vs

year	age	plhiv	know_status	on_art	plhiv_virally_suppressed	prob_art_if_dx	virally_suppressed_on_art	vs_assumed_value
2011	adults	100	73.2277	37.6375	nan	0.513979	80	yes
2012	adults	100	76.423	46.3159	42.1013	0.606046	91	no
2013	adults	100	78.7843	52.9497	47.6735	0.672084	90	no
2014	adults	100	80.8733	59.2378	51.5664	0.732477	87	no
2015	adults	100	82.7952	64.1071	57.269	0.774285	89	no
2016	adults	100	85.3839	71.6873	65.3256	0.839588	91	no
2017	adults	100	88.3281	78.056	69.322	0.883705	89	no
2018	adults	100	90.6581	84.2257	76.8029	0.929047	91	no
2019	adults	100	92.1484	85.4227	79.9867	0.927012	94	no

Only first 10 rows of 32 are shown.

scaleup_parameters

parameter	target_value	min_value	max_value
reduction_in_hiv_beta	0.9	1	0
prob_prep_for_fsw_after_hiv_test	0.5	0	1
prob_prep_for_agyw	0.1	0	1
probability_of_being_retained_on_prep_every_3_months	0.75	0	1
probability_of_being_retained_on_art_every_3_months	1	0	1
prob_circ_after_hiv_test	0.25	0	1
annual_testing_rate_adults	0.4	0	1
prob_hiv_test_at_anc_or_delivery	0.95	0	1
prob_hiv_test_for_newborn_infant	0.95	0	1
virally_suppressed_on_art	95	0	100

Labour

Name	Description	Type	Value
intercept_parity_lr2010	intercept value for linear regression equation predicating womens parity at 2010 baseline	List	[-2.81, -2.81]
effect_age_parity_lr2010	effect of an increase in age by 1 year in the linear regression equation predicating womens parity at 2010 baseline	List	[0.21, 0.21]
effect_mar_stat_2_parity_lr2010	effect of a change in marriage status from comparison (level 1) in the linear regression equation predicating womans parity at 2010 baseline	List	[0.84, 0.84]
effect_mar_stat_3_parity_lr2010	effect of a change in marriage status from comparison (level 1) in the linear regression equation predicating womans parity at 2010 baseline	List	[0.14, 0.14]
effect_wealth_lev_4_parity_lr2010	effect of an increase in wealth level in the linear regression equation predicating womans parity at 2010 base line	List	[-0.09, -0.09]
effect_wealth_lev_3_parity_lr2010	effect of an increase in wealth level in the linear regression equation predicating womans parity at 2010 base line	List	[-0.18, -0.18]
effect_wealth_lev_2_parity_lr2010	effect of an increase in wealth level in the linear regression equation predicating womans parity at 2010 base line	List	[-0.22, -0.22]
effect_wealth_lev_1_parity_lr2010	effect of an increase in wealth level in the linear regression equation predicating womans parity at 2010 base line	List	[-0.48, -0.48]
effect_edu_lev_2_parity_lr2010	effect of an increase in education level in the linear regression equation predicating womans parity at 2010 base line	List	[-0.33, -0.33]
effect_edu_lev_3_parity_lr2010	effect of an increase in education level in the linear regression equation predicating womans parity at 2010 base line	List	[-1, -1]
effect_rural_parity_lr2010	effect of rural living in the linear regression equation predicating womans parity at 2010 base line	List	[0.19, 0.19]
prob_previous_caesarean_at_baseline	probability of previously having delivered via caesarean section at baseline	List	[0.046, 0.046]
risk_post_term_labour	risk of remaining pregnant past 42 weeks	List	[0.077, 0.077]
rr_potl_bmi_30_35	effect of maternal BMI being between 30 and 35 on risk of post term labour	List	[1.42, 1.42]
rr_potl_bmi_35+	effect of maternal BMI being between above 35 on risk of post term labour	List	[1.55, 1.55]
list_limits_for_defining_term_status	List of number of days of gestation used to define term, early preterm, late preterm and post term delivery	List	[[259, 293, 148, 230, 231, 258, 294], [259, 293, 148, 230, 231, 258, 294]]
allowed_interventions	list of interventions allowed to run, used in analysis	List	[[‘prophylactic_labour_interventions’, ‘assessment_and_treatment_of_severe_pre_eclampsia’, ‘assessment_and_treatment_of_obstructed_labour’, ‘assessment_and_treatment_of_maternal_sepsis’, ‘assessment_and_treatment_of_hypertension’, ‘assessment_and_treatment_of_eclampsia’, ‘assessment_and_plan_for_referral_antepartum_haemorrhage’, ‘assessment_and_plan_for_referral_uterine_rupture’, ‘active_management_of_the_third_stage_of_labour’, ‘assessment_and_treatment_of_pph_retained_placenta’, ‘assessment_and_treatment_of_pph_uterine_atony’], [‘prophylactic_labour_interventions’, ‘assessment_and_treatment_of_severe_pre_eclampsia’, ‘assessment_and_treatment_of_obstructed_labour’, ‘assessment_and_treatment_of_maternal_sepsis’, ‘assessment_and_treatment_of_hypertension’, ‘assessment_and_treatment_of_eclampsia’, ‘assessment_and_plan_for_referral_antepartum_haemorrhage’, ‘assessment_and_plan_for_referral_uterine_rupture’, ‘active_management_of_the_third_stage_of_labour’, ‘assessment_and_treatment_of_pph_retained_placenta’, ‘assessment_and_treatment_of_pph_uterine_atony’]]
mean_birth_weights	list of mean birth weights from gestational age at birth 24-41 weeks	List	[[657, 746, 851, 966, 1096, 1240, 1440, 1641, 1841, 2041, 2242, 2442, 2736, 2856, 2995, 3036, 3117, 3136], [657, 746, 851, 966, 1096, 1240, 1440, 1641, 1841, 2041, 2242, 2442, 2736, 2856, 2995, 3036, 3117, 3136]]
standard_deviation_birth_weights	list of standard deviations associated with mean birth weights from gestational age at birth 24-41 weeks	List	[[113, 140, 169, 196, 218, 235, 274, 312, 351, 390, 428, 460, 467, 398, 356, 351, 396, 351], [113, 140, 169, 196, 218, 235, 274, 312, 351, 390, 428, 460, 467, 398, 356, 351, 396, 351]]
residual_prob_of_macrosomia	probability that those allocated to be normal birth weight and above will be macrosomic (>4kg)	List	[0.057, 0.057]
prob_obstruction_cpd	risk of a woman developing obstructed labour secondary to cephalopelvic disproportion	List	[0.012, 0.022]
rr_obstruction_cpd_stunted_mother	relative risk of obstruction secondary to CPD in mothers who are stunted	List	[2.4, 2.4]
rr_obstruction_foetal_macrosomia	relative risk of obstruction secondary to CPD in mothers who are carrying a macrosomic foetus	List	[3.3, 3.3]
prob_obstruction_malpos_malpres	risk of a woman developing obstructed labour secondary to malposition or malpresentation	List	[0.005, 0.009]
prob_obstruction_other	risk of a woman developing obstructed labour secondary to other causes	List	[0.0015, 0.0027]
prob_placental_abruption_during_labour	probability of a woman developing placental abruption during labour	List	[0.0005, 0.0005]
prob_aph_placenta_praevia_labour	probability of a woman with placenta praevia experiencing an APH during labour	List	[0.25, 0.25]
prob_aph_placental_abruption_labour	probability of a woman with placental abruption experiencing an APH during labour	List	[0.9, 0.9]
rr_placental_abruption_hypertension	Relative risk of placental abruption in women with hypertension	List	[2.2, 2.2]
rr_placental_abruption_previous_cs	Relative risk of placental abruption in women who delivered previously via caesarean section	List	[1.3, 1.3]
severity_maternal_haemorrhage	probability a maternal hemorrhage is non-severe (<1000mls) or severe (>1000mls)	List	[[0.8, 0.2], [0.8, 0.2]]
cfr_aph	case fatality rate for antepartum haemorrhage during labour	List	[0.11, 0.04]
prob_sepsis_chorioamnionitis	risk of sepsis following chorioamnionitis infection	List	[0.0002, 0.00018]
rr_sepsis_chorio_prom	relative risk of chorioamnionitis following PROM	List	[1.76, 1.76]
prob_sepsis_endometritis	risk of sepsis following endometritis	List	[6.9e-05, 6.2e-05]
rr_sepsis_endometritis_post_cs	relative risk of endometritis following caesarean delivery	List	[12.1, 12.1]
prob_sepsis_urinary_tract	risk of sepsis following urinary tract infection	List	[5.4e-05, 5.4e-05]
prob_sepsis_skin_soft_tissue	risk of sepsis following skin or soft tissue infection	List	[3.9e-05, 3.5e-05]
rr_sepsis_sst_post_cs	relative risk of skin/soft tissue sepsis following caesarean delivery	List	[3.9, 3.9]
cfr_sepsis	case fatality rate for sepsis during labour	List	[0.75, 0.49]
cfr_pp_sepsis	case fatality rate for sepsis following delivery	List	[0.75, 0.49]
prob_uterine_rupture	probability of a uterine rupture during labour	List	[0.0011, 0.0005]
rr_ur_parity_2	relative risk of uterine rupture in women who have delivered 2 times previously	List	[2.74, 2.74]
rr_ur_parity_3_or_4	relative risk of uterine rupture in women who have delivered 3-4 times previously	List	[4.89, 4.89]
rr_ur_parity_5+	relative risk of uterine rupture in women who have delivered > 5 times previously	List	[7.57, 7.57]
rr_ur_prev_cs	relative risk of uterine rupture in women who have previously delivered via caesarean section	List	[2.02, 2.02]
rr_ur_obstructed_labour	relative risk of uterine rupture in women who have been in obstructed labour	List	[23.6, 23.6]
cfr_uterine_rupture	case fatality rate for uterine rupture in labour	List	[0.65, 0.5]
prob_progression_gest_htn	probability of gestational hypertension progressing to severe gestational hypertensionduring/after labour	List	[0.036, 0.036]
prob_progression_severe_gest_htn	probability of severe gestational hypertension progressing to severe pre-eclampsia during/after labour	List	[0.13, 0.13]
prob_progression_mild_pre_eclamp	probability of mild pre-eclampsia progressing to severe pre-eclampsia during/after labour	List	[0.14, 0.14]
prob_progression_severe_pre_eclamp	probability of severe pre-eclampsia progressing to eclampsia during/after labour	List	[0.29, 0.29]
cfr_eclampsia	case fatality rate for eclampsia during labours	List	[0.028, 0.03]
cfr_severe_pre_eclamp	case fatality rate for severe pre eclampsia during labour	List	[0.018, 0.018]
prob_ip_still_birth	baseline probability of intrapartum still birth	List	[0.006, 0.005]
rr_still_birth_maternal_death	relative risk of still birth in mothers who have died during labour	List	[180, 180]
rr_still_birth_ur	relative risk of still birth in mothers experiencing uterine rupture	List	[56.6, 56.6]
rr_still_birth_ol	relative risk of still birth in mothers experiencing obstructed labour	List	[4.5, 4.5]
rr_still_birth_aph	relative risk of still birth in mothers experiencing antepartum haemorrhage	List	[2.1, 2.1]
rr_still_birth_hypertension	relative risk of still birth in mothers experiencing hypertension	List	[4.5, 4.5]
rr_still_birth_sepsis	relative risk of still birth in mothers experiencing intrapartum sepsis	List	[2, 2]
rr_still_birth_multiple_pregnancy	relative risk of still birth in mothers pregnant with twins	List	[3, 3]
prob_both_twins_ip_still_birth	probability that if this mother will experience still birth, and she is pregnant with twins, that neither baby will survive	List	[0.8, 0.8]
prob_pph_uterine_atony	risk of pph after experiencing uterine atony	List	[0.006, 0.011]
rr_pph_ua_hypertension	relative risk risk of pph after secondary to uterine atony in hypertensive women	List	[1.84, 1.84]
rr_pph_ua_multiple_pregnancy	relative risk risk of pph after secondary to uterine atony in women pregnant with twins	List	[2.16, 2.16]
rr_pph_ua_placental_abruption	relative risk risk of pph after secondary to uterine atony in women with placental abruption	List	[2.74, 2.74]
rr_pph_ua_macrosomia	relative risk risk of pph after secondary to uterine atony in women with macrosomic foetus	List	[1.46, 1.46]
rr_pph_ua_diabetes	risk of pph after experiencing uterine atony	List	[1.22, 1.22]
prob_pph_retained_placenta	risk of pph after experiencing retained placenta	List	[0.001, 0.0016]
prob_pph_other_causes	risk of pph after experiencing other pph causes	List	[0.0007, 0.001]
cfr_pp_pph	case fatality rate for postpartum haemorrhage	List	[0.22, 0.08]
rr_death_from_haem_with_anaemia	relative risk increase of death in women who are anaemic at time of PPH	List	[1.5, 1.5]
odds_deliver_in_health_centre	odds of a woman delivering in a health centre compared to a hospital	List	[0.69, 1.08]
rrr_hc_delivery_age_20_24	relative risk ratio for a woman aged 20-24 delivering in a health centre compared to a hospital	List	[0.79, 1]
rrr_hc_delivery_age_25_29	relative risk ratio for a woman aged 25-29 delivering in a health centre compared to a hospital	List	[0.5, 0.56]
rrr_hc_delivery_age_30_34	relative risk ratio for a woman aged 30-34 delivering in a health centre compared to a hospital	List	[0.27, 0.32]
rrr_hc_delivery_age_35_39	relative risk ratio for a woman aged 35-39 delivering in a health centre compared to a hospital	List	[0.13, 0.14]
rrr_hc_delivery_age_40_44	relative risk ratio for a woman aged 40-44 delivering in a health centre compared to a hospital	List	[0.06, 0.07]
rrr_hc_delivery_age_45_49	relative risk ratio for a woman aged 45-49 delivering in a health centre compared to a hospital	List	[0.02, 0.03]
rrr_hc_delivery_wealth_4	relative risk ratio of a woman at wealth level 4 delivering at health centre compared to a hospital	List	[0.82, 0.79]
rrr_hc_delivery_wealth_3	relative risk ratio of a woman at wealth level 3 delivering at health centre compared to a hospital	List	[0.77, 0.73]
rrr_hc_delivery_wealth_2	relative risk ratio of a woman at wealth level 2 delivering at health centre compared to a hospital	List	[0.62, 0.58]
rrr_hc_delivery_wealth_1	relative risk ratio of a woman at wealth level 1 delivering at health centre compared to a hospital	List	[0.55, 0.43]
rrr_hc_delivery_parity_3_to_4	relative risk ratio for a woman with a parity of 3-4 delivering in a health centre compared toa hospital	List	[2, 1.85]
rrr_hc_delivery_parity_>4	relative risk ratio of a woman with a parity >4 delivering in health centre compared to a hospital	List	[3.9, 3.8]
rrr_hc_delivery_rural	relative risk ratio of a married woman delivering in a health centre compared to a hospital	List	[1.99, 1.81]
rrr_hc_delivery_married	relative risk ratio of a married woman delivering in a health centre compared to a hospital	List	[1.3, 1.42]
odds_deliver_at_home	odds of a woman delivering at home compared to a hospital	List	[0.37, 0.09]
rrr_hb_delivery_age_20_24	relative risk ratio for a woman aged 20-24 delivering at home compared to a hospital	List	[1.42, 1]
rrr_hb_delivery_age_25_29	relative risk ratio for a woman aged 25-29 delivering at home compared to a hospital	List	[1, 0.58]
rrr_hb_delivery_age_30_34	relative risk ratio for a woman aged 30-34 delivering at home compared to a hospital	List	[0.42, 0.25]
rrr_hb_delivery_age_35_39	relative risk ratio for a woman aged 35-39 delivering at home compared to a hospital	List	[0.24, 0.16]
rrr_hb_delivery_age_40_44	relative risk ratio for a woman aged 40-44 delivering at home compared to a hospital	List	[0.12, 0.07]
rrr_hb_delivery_age_45_49	relative risk ratio for a woman aged 45-49 delivering at home compared to a hospital	List	[0.05, 0.04]
rrr_hb_delivery_rural	relative risk ratio of a rural delivering at home compared to a hospital	List	[1.73, 1]
rrr_hb_delivery_primary_education	relative risk ratio of a woman with a primary education delivering at home compared to a hospital	List	[0.76, 0.79]
rrr_hb_delivery_secondary_education	relative risk ratio of a woman with a secondary education delivering at home compared to a hospital	List	[0.46, 0.51]
rrr_hb_delivery_wealth_4	relative risk ratio of a woman at wealth level 4 delivering at home compared to a hospital	List	[0.82, 0.74]
rrr_hb_delivery_wealth_3	relative risk ratio of a woman at wealth level 3 delivering at home compared to a hospital	List	[0.72, 0.68]
rrr_hb_delivery_wealth_2	relative risk ratio of a woman at wealth level 2 delivering at home compared to a hospital	List	[0.41, 0.49]
rrr_hb_delivery_wealth_1	relative risk ratio of a woman at wealth level 1 delivering at home compared to a hospital	List	[0.2, 0.17]
rrr_hb_delivery_parity_3_to_4	relative risk ratio for a woman with a parity of 3-4 delivering at home compared toa hospital	List	[2.4, 1]
rrr_hb_delivery_parity_>4	relative risk ratio of a woman with a parity >4 delivering at home compared to a hospital	List	[5.25, 1]
rrr_hb_delivery_married	relative risk ratio of a married woman delivering in a home compared to a hospital	List	[0.63, 1]
probability_delivery_hospital	probability of delivering in a hospital	List	[0.32, 0.4]
prob_timings_pnc	probabilities that a woman who will receive a PNC check will receive care <48hrs post birth or > 48hrs post birth	List	[[0.85, 0.15], [0.88, 0.12]]
odds_will_attend_pnc	baseline odss a woman will seek PNC for her and her newborn following delivery	List	[0.9, 0.9]
or_pnc_age_30_35	odds ratio for women aged 30-35 attending PNC	List	[1.75, 1.75]
or_pnc_age_>35	odds ratio for women aged > 35 attending PNC	List	[1.86, 1.86]
or_pnc_rural	odds ratio for women who live rurally attending PNC	List	[0.55, 0.55]
or_pnc_wealth_level_1	odds ratio for women from the highest wealth level attending PNC	List	[0.72, 0.72]
or_pnc_anc4+	odds ratio for women who attended ANC4+ attending PNC	List	[1.2, 1.2]
or_pnc_caesarean_delivery	odds ratio for women who delivered by caesarean attending PNC	List	[1.93, 1.93]
or_pnc_facility_delivery	odds ratio for women who delivered in a health facility attending PNC	List	[1.91, 1.91]
or_pnc_parity_>4	odds ratio for women with a parity of >4 attending PNC	List	[0.03, 0.03]
probs_of_attending_pn_event_by_day	probabilities used in a weighted random draw to determine when a woman will attend the postnatal event	List	[[0.4, 0.3, 0.2, 0.05, 0.05], [0.4, 0.3, 0.2, 0.05, 0.05]]
prob_careseeking_for_complication	probability of a woman seeking skilled assistance after developing a complication at a home birth	List	[0.782, 0.782]
prob_careseeking_for_complication_pn	probability of a woman seeking skilled assistance after developing a postnatal complication following a home birth	List	[0.782, 0.782]
test_care_seeking_probs	dummy probabilities of delivery care seeking used in testing	List	[[0.33, 0.33, 0.34], [0.33, 0.33, 0.34]]
prob_delivery_modes_ec	probabilities that a woman admitted with eclampsia will deliver normally, via caesarean or via assisted vaginal delivery	List	[[0, 0, 1], [0, 0, 1]]
prob_delivery_modes_spe	probabilities that a woman admitted with severe pre-eclampsia will deliver normally, via caesarean or via assisted vaginal delivery	List	[[0.05, 0.05, 0.9], [0.05, 0.05, 0.9]]
residual_prob_avd	probabilities that a woman will deliver via assisted vaginal delivery for an indication not explicitly modelled	List	[0.128, 0.128]
residual_prob_caesarean	probabilities that a woman will deliver via caesarean section for an indication not explicitly modelled	List	[0.0188, 0.022]
prob_adherent_ifa	probability that a woman started on postnatal IFA will be adherent	List	[0.37, 0.34]
effect_of_ifa_for_resolving_anaemia	relative effect of iron and folic acid on anaemia status	List	[0.7, 0.7]
number_ifa_tablets_required_postnatally	total number of iron and folic acid tablets required during postnatal period	List	[93, 93]
treatment_effect_maternal_infection_clean_delivery	Effect of clean delivery practices on risk of maternal infection	List	[0.4, 0.4]
treatment_effect_maternal_chorio_abx_prom	Relative effect of antibiotics for premature rupture of membranes on maternal risk of chorioamnionitis prior to birth	List	[0.66, 0.66]
treatment_effect_amtsl	relative risk of severe postpartum haemorrhage following active management of the third stage of labour	List	[0.34, 0.34]
prob_haemostatis_uterotonics	probability of uterotonics stopping a postpartum haemorrhage due to uterine atony	List	[0.57, 0.57]
prob_successful_manual_removal_placenta	probability of manual removal of retained products arresting a post partum haemorrhage	List	[0.75, 0.75]
success_rate_pph_surgery	probability of surgery for postpartum haemorrhage being successful	List	[0.79, 0.79]
pph_treatment_effect_surg_md	effect of surgery on maternal death due to postpartum haemorrhage	List	[0.25, 0.25]
pph_treatment_effect_hyst_md	effect of hysterectomy on maternal death due to postpartum haemorrhage	List	[0.25, 0.25]
pph_bt_treatment_effect_md	effect of blood transfusion treatment for postpartum haemorrhage on risk of maternal death	List	[0.4, 0.4]
sepsis_treatment_effect_md	effect of treatment for sepsis on risk of maternal death	List	[0.2, 0.2]
success_rate_uterine_repair	probability repairing a ruptured uterus surgically	List	[0.83, 0.83]
prob_successful_assisted_vaginal_delivery	probability of successful assisted vaginal delivery	List	[0.7, 0.7]
ur_repair_treatment_effect_md	effect of surgical uterine repair treatment for uterine rupture on risk of maternal death	List	[0.25, 0.25]
ur_treatment_effect_bt_md	effect of blood transfusion treatment for uterine rupture on risk of maternal death	List	[0.4, 0.4]
ur_hysterectomy_treatment_effect_md	effect of blood hysterectomy for uterine rupture on risk of maternal death	List	[0.25, 0.25]
eclampsia_treatment_effect_severe_pe	effect of treatment for severe pre eclampsia on risk of eclampsia	List	[0.41, 0.41]
eclampsia_treatment_effect_md	effect of treatment for eclampsia on risk of maternal death	List	[0.4, 0.4]
anti_htns_treatment_effect_md	effect of IV anti hypertensive treatment on risk of death secondary to severe pre-eclampsia/eclampsia stillbirth	List	[0.5, 0.5]
anti_htns_treatment_effect_progression	effect of IV anti hypertensive treatment on risk of progression from mild to severe gestational hypertension	List	[0.49, 0.49]
aph_bt_treatment_effect_md	effect of blood transfusion treatment for antepartum haemorrhage on risk of maternal death	List	[0.4, 0.4]
treatment_effect_blood_transfusion_anaemia	effect of blood transfusion treatment for severe anaemia	List	[0.9, 0.9]
aph_cs_treatment_effect_md	effect of caesarean section for antepartum haemorrhage on risk of maternal death	List	[0.25, 0.25]
treatment_effect_avd_still_birth	effect of assisted vaginal delivery on risk of intrapartum still birth	List	[0.55, 0.55]
treatment_effect_cs_still_birth	effect of caesarean section delivery on risk of intrapartum still birth	List	[0.25, 0.25]
prob_hcw_avail_iv_abx	average probability that a health facility providing EmONC care has a HCW available that can delivery signal function - parenteral antibiotics	List	[0.99, 0.99]
prob_hcw_avail_uterotonic	average probability that a health facility providing EmONC care has a HCW available that can delivery signal function - parenteral uterotonics	List	[0.99, 0.99]
prob_hcw_avail_anticonvulsant	average probability that a health facility providing EmONC care has a HCW available that can delivery signal function - parenteral anticonvulsants	List	[0.93, 0.93]
prob_hcw_avail_man_r_placenta	average probability that a health facility providing EmONC care has a HCW available that can delivery signal function - manual removal of retained placenta	List	[0.82, 0.82]
prob_hcw_avail_avd	average probability that a health facility providing EmONC care has a HCW available that can delivery signal function - assisted vaginal delivery	List	[0.46, 0.46]
prob_hcw_avail_blood_tran	average probability that a health facility providing EmONC care has a HCW available that can delivery signal function - blood transfusion	List	[0.86, 0.86]
prob_hcw_avail_surg	average probability that a health facility providing EmONC care has a HCW available that can delivery signal function - obstetric surgery	List	[0.74, 0.74]
prob_hcw_avail_retained_prod	average probability that a health facility providing EmONC care has a HCW available that can delivery signal function - removal of retained products of conception	List	[0.49, 0.49]
prob_hcw_avail_neo_resus	average probability that a health facility providing EmONC care has a HCW available that can delivery signal function - neonatal resuscitation	List	[0.98, 0.98]
mean_hcw_competence_hc	mean competence of HCW at delivering EmONC care at a health centre. A draw below this level prevents intervention delivery	List	[[0.602, 0.602], [0.602, 0.602]]
mean_hcw_competence_hp	mean competence of HCW at delivering EmONC care at a hospital. A draw below this level prevents intervention delivery	List	[[0.662, 0.662], [0.662, 0.662]]
prob_intervention_delivered_anaemia_assessment_pnc	probability a woman will have their Hb levels checked during PNC given that the HSI has ran and the consumables are available (proxy for clinical quality)	List	[0.14, 0.18]
analysis_year	Year on which changes in parameters as part of analysis should be enacted (1st day, 1st month)	Integer	2023
la_analysis_in_progress	Used within the pregnancy_helper_function to signify that labour/postnatal analysis is currently being conducted	Boolean	False
alternative_bemonc_availability	parameter used in analysis to allow manipulation of coverage of BEmONC interventions	Boolean	False
alternative_cemonc_availability	parameter used in analysis to allow manipulation of coverage of CEmONC interventions	Boolean	False
bemonc_availability	set probability of BEmONC intervention being delivered during analysis	Real	1.0
cemonc_availability	set probability of CEmONC intervention being delivered during analysis	Real	1.0
bemonc_cons_availability	set probability of BEmONC consumables being available	Real	1.0
cemonc_cons_availability	set probability of CEmONC consumables being available	Real	1.0
alternative_pnc_coverage	Signals within the analysis event that an alternative level of PNC coverage has been determined following the events run	Boolean	False
alternative_pnc_quality	Signals within the analysis event that an alternative level of PNC quality has been determined following the events run	Boolean	False
pnc_availability_odds	Target odds of maternal PNC coverage when analysis is being conducted - only applied ifalternative_pnc_coverage is true	Real	3.0
pnc_availability_probability	Target probability of quality/consumables when analysis is being conducted - only applied if alternative_pnc_coverage is true	Real	1.0
sba_sens_analysis_max	Signals that max coverage of SBA is being forced for sensitivity analysis	Boolean	False
pnc_sens_analysis_max	Signals that max coverage of PNC is being forced for sensitivity analysis	Boolean	False
pnc_sens_analysis_min	Signals that min coverage of SBA is being forced for sensitivity analysis	Boolean	False

Lifestyle

Name	Description	Type	Value
init_p_urban	initial proportion urban	Dictionary	…
init_p_wealth_urban	List of probabilities of category given urban	List	[0.75, 0.16, 0.05, 0.02, 0.02]
init_p_wealth_rural	List of probabilities of category given rural	List	[0.11, 0.21, 0.22, 0.23, 0.23]
init_p_bmi_urban_m_not_high_sugar_age1529_not_tob_wealth1	List of probabilities of bmi categories for urban men age 15-29 with not high sugar, not tobacco, wealth level 1	List	[0.06, 0.8, 0.12, 0.01, 0.01]
init_or_higher_bmi_f	odds ratio higher BMI if female	Real	3.0
init_or_higher_bmi_rural	odds ratio higher BMI if rural	Real	0.6
init_or_higher_bmi_high_sugar	odds ratio higher BMI if high sugar intake	Real	1.1
init_or_higher_bmi_age3049	odds ratio higher BMI if age 30-49	Real	1.8
init_or_higher_bmi_agege50	odds ratio higher BMI if age ge 50	Real	2.7
init_or_higher_bmi_tob	odds ratio higher BMI if use tobacco	Real	0.7
init_or_higher_bmi_per_higher_wealth_level	odds ratio for higher initial bmi category per higher wealth level	Real	0.85
init_p_high_sugar	initital proportion with high sugar intake	Real	0.4
init_p_high_salt_urban	initital proportion with high salt intake	Real	0.2
init_or_high_salt_rural	odds ratio high salt if rural	Real	1.5
init_p_ex_alc_m	initital proportion of men with excess alcohol use	Real	0.15
init_p_ex_alc_f	initital proportion of women with excess alcohol use	Real	0.01
init_p_low_ex_urban_m	initital proportion of men with low exercise urban	Real	0.32
init_or_low_ex_rural	odds ratio low exercise rural	Real	0.4
init_or_low_ex_f	odds ratio low exercise female	Real	0.6
init_p_tob_age1519_m_wealth1	initial proportion of 15-19 year old men using tobacco, wealth level 1	Real	0.01
init_or_tob_f	odds ratio tobacco use females	Real	0.2
init_or_tob_age2039_m	odds ratio tobacco use age2039 in men	Real	4.0
init_or_tob_agege40_m	odds ratio tobacco use age40+ in men	Real	6.0
init_or_tob_wealth2	odds ratio tobacco use wealth level 2	Real	2.0
init_or_tob_wealth3	odds ratio tobacco use wealth level 3	Real	3.0
init_or_tob_wealth4	odds ratio tobacco use wealth level 4	Real	4.0
init_or_tob_wealth5	odds ratio tobacco use wealth level 5	Real	5.0
init_dist_mar_stat_age1520	proportions never, current, div_wid age 15-20 baseline	List	[0.7, 0.3, 0]
init_dist_mar_stat_age2030	proportions never, current, div_wid age 20-30 baseline	List	[0.15, 0.8, 0.05]
init_dist_mar_stat_age3040	proportions never, current, div_wid age 30-40 baseline	List	[0.05, 0.7, 0.25]
init_dist_mar_stat_age4050	proportions never, current, div_wid age 40-50 baseline	List	[0.03, 0.5, 0.47]
init_dist_mar_stat_age5060	proportions never, current, div_wid age 50-60 baseline	List	[0.03, 0.3, 0.67]
init_dist_mar_stat_agege60	proportions never, current, div_wid age 60+ baseline	List	[0.03, 0.2, 0.77]
init_age2030_w5_some_ed	proportions of low wealth 20-30 year olds with some education at baseline	Real	0.97
init_prop_age2030_w5_some_ed_sec	proportion of low wealth aged 20-30 with some education who have secondary education at baseline	Real	0.1
init_p_unimproved_sanitation_urban	initial probability of unimproved_sanitation given urban	Real	0.04
init_or_unimproved_sanitation_rural	initial odds ratio of unimproved_sanitation if rural	Real	4.5
init_p_no_clean_drinking_water_urban	initial probability of no_clean_drinking_water given urban	Real	0.017
init_or_no_clean_drinking_water_rural	initial odds ratio of no clean drinking_water if rural	Real	8.6
init_p_wood_burn_stove_urban	initial probability of wood_burn_stove given urban	Real	0.257
init_or_wood_burn_stove_rural	initial odds ratio of wood_burn_stove if rural	Real	40.0
init_p_no_access_handwashing_wealth1	initial probability of no_access_handwashing given wealth 1	Real	0.478
init_or_no_access_handwashing_per_lower_wealth	initial odds ratio of no_access_handwashing per lower wealth level	Real	1.06
init_prop_primary_edu	proportion of starting primary education at baseline age 5-12	Real	0.5
init_rp_some_ed_age0513	relative prevalence of some education at baseline age 5-13	Real	1.01
init_rp_some_ed_age1320	relative prevalence of some education at baseline age 13-20	Real	1.0
init_rp_some_ed_age2030	relative prevalence of some education at baseline age 20-30	Real	1.0
init_rp_some_ed_age3040	relative prevalence of some education at baseline age 30-40	Real	1.0
init_rp_some_ed_age4050	relative prevalence of some education at baseline age 40-50	Real	0.9
init_rp_some_ed_age5060	relative prevalence of some education at baseline age 50-60	Real	0.9
init_rp_some_ed_per_higher_wealth	relative prevalence of some education at baseline per higher wealth level	Real	1.005
init_rp_some_ed_sec_age1320	relative prevalence of secondary education age 15-20	Real	1.0
init_rp_some_ed_sec_age3040	relative prevalence of secondary education age 30-40	Real	0.8
init_rp_some_ed_sec_age4050	relative prevalence of secondary education age 40-50	Real	0.6
init_rp_some_ed_sec_age5060	relative prevalence of secondary education age 50-60	Real	0.4
init_rp_some_ed_sec_agege60	relative prevalence of secondary education age 60+	Real	0.2
init_rp_some_ed_agege60	relative prevalence of some education at baseline age age 60+	Real	0.9
init_rp_some_ed_sec_per_higher_wealth	relative prevalence of secondary education per higher wealth level	Real	1.48
r_urban	probability per 3 months of change from rural to urban	Real	0.0005
r_rural	probability per 3 months of change from urban to rural	Real	1e-05
r_higher_bmi	probability per 3 months of increase in bmi category if rural male age15-29 not using tobacoo with wealth level 1 with not high sugar intake	Real	0.0005
rr_higher_bmi_urban	probability per 3 months of increase in bmi category if	Real	1.5
rr_higher_bmi_f	rate ratio for increase in bmi category for females	Real	3.0
rr_higher_bmi_age3049	rate ratio for increase in bmi category for age 30-49	Real	1.8
rr_higher_bmi_agege50	rate ratio for increase in bmi category for age ge 50	Real	2.7
rr_higher_bmi_tob	rate ratio for increase in bmi category for tobacco users	Real	0.7
rr_higher_bmi_per_higher_wealth	rate ratio for increase in bmi category per higher wealth level	Real	0.85
rr_higher_bmi_high_sugar	rate ratio for increase in bmi category for high sugar intake	Real	1.2
r_lower_bmi	probability per 3 months of decrease in bmi category in non tobacco users	Real	0.001
rr_lower_bmi_tob	rate ratio for lower bmi category for tobacco users	Real	1.4
rr_lower_bmi_pop_advice_weight	probability per 3 months of decrease in bmi category given population advice/campaign on weight	Real	1.1
r_high_salt_urban	probability per 3 months of high salt intake if urban	Real	0.003
rr_high_salt_rural	rate ratio for high salt if rural	Real	1.5
r_not_high_salt	probability per 3 months of not high salt intake	Real	0.0001
rr_not_high_salt_pop_advice_salt	probability per 3 months of not high salt given population advice/campaign on salt	Real	1.1
r_high_sugar	probability per 3 months of high sugar intake	Real	0.0001
r_not_high_sugar	probability per 3 months of not high sugar intake	Real	0.0001
rr_not_high_sugar_pop_advice_sugar	probability per 3 months of not high sugar given population advice/campaign on sugar	Real	1.1
r_low_ex	probability per 3 months of change from not low exercise to low exercise	Real	0.001
r_not_low_ex	probability per 3 months of change from low exercise to not low exercie	Real	0.0001
rr_not_low_ex_pop_advice_exercise	probability per 3 months of not low exercise population advice/campaign on exercise	Real	1.1
rr_low_ex_f	risk ratio for becoming low exercise if female rather than male	Real	0.6
rr_low_ex_urban	risk ratio for becoming low exercise if urban rather than rural	Real	2.0
r_tob	probability per 3 months of change from not using tobacco to using tobacco if male age 15-19 wealth level 1	Real	0.0004
r_not_tob	probability per 3 months of change from tobacco using to not tobacco using	Real	0.0001
rr_tob_f	rate ratio tobacco if female	Real	0.1
rr_tob_age2039	risk ratio for tobacco using if age 20-39 compared with 15-19	Real	1.2
rr_tob_agege40	risk ratio for tobacco using if age >= 40 compared with 15-19	Real	1.5
rr_tob_wealth	risk ratio for tobacco using per 1 higher wealth level (higher wealth level = lower wealth)	Real	1.3
rr_not_tob_pop_advice_tobacco	probability per 3 months of quitting tobacco given population advice/campaign on tobacco	Real	1.1
r_ex_alc	probability per 3 months of change from not excess alcohol to excess alcohol	Real	0.003
r_not_ex_alc	probability per 3 months of change from excess alcohol to not excess alcohol	Real	0.0001
rr_ex_alc_f	risk ratio for becoming excess alcohol if female rather than male	Real	0.07
rr_not_ex_alc_pop_advice_alcohol	probability per 3 months of not excess alcohol given population advice/campaign on alcohol	Real	1.1
r_mar	probability per 3 months of marriage when age 15-30	Real	0.03
r_div_wid	probability per 3 months of becoming divorced or widowed, amongst those married	Real	0.01
r_stop_ed	probabilities per 3 months of stopping education if wealth level 5	Real	0.007
rr_stop_ed_lower_wealth	relative rate of stopping education per 1 lower wealth quantile	Real	1.5
p_ed_primary	probability at age 5 that start primary education if wealth level 5	Real	0.9
rp_ed_primary_higher_wealth	relative probability of starting school per 1 higher wealth level	Real	1.1
p_ed_secondary	probability at age 13 that start secondary education at 13 if in primary education and wealth level 5	Real	0.8
rp_ed_secondary_higher_wealth	relative probability of starting secondary school per 1 higher wealth level	Real	1.05
r_improved_sanitation	probability per 3 months of change from unimproved_sanitation true to false	Real	0.001
r_clean_drinking_water	probability per 3 months of change from drinking_water true to false	Real	0.001
r_non_wood_burn_stove	probability per 3 months of change from wood_burn_stove true to false	Real	0.001
r_access_handwashing	probability per 3 months of change from no access hand washing true to false	Real	0.001
start_date_campaign_exercise_increase	Date of campaign start for increased exercise	Date	2010-07-01 00:00:00
start_date_campaign_quit_smoking	Date of campaign start to quit smoking	Date	2010-07-01 00:00:00
start_date_campaign_alcohol_reduction	Date of campaign start for alcohol reduction	Date	2010-07-01 00:00:00
proportion_of_men_that_are_assumed_to_be_circumcised_at_birth	Proportion of men that are assumed to be circumcised at birth.The men are assumed to be circumcised at birth.	Real	0.2128
proportion_of_men_circumcised_at_initiation	Proportion of men (of all ages) that are assumed to be circumcised at the initiation of thesimulation.	Real	0.2128
proportion_female_sex_workers	proportion of women aged 15-49 years who are sex workers	Real	0.0069
fsw_transition	proportion of sex workers that stop being a sex worker each year	Real	0.18181818181818182

init_p_urban

prop_urban

Chitipa	Karonga	Nkhata Bay	Rumphi	Mzimba	Likoma	Mzuzu	Mzuzu City	Kasungu	Nkhotakota	Ntchisi	Dowa	Salima	Lilongwe	Lilongwe City	Mchinji	Dedza	Ntcheu	Mangochi	Machinga	Zomba	Zomba City	Chiradzulu	Blantyre	Blantyre City	Mwanza	Thyolo	Mulanje	Phalombe	Chikwawa	Nsanje	Balaka	Neno
0.1846	0.2644	0.1716	0.2188	0.0386	0.1503	0	1	0.2029	0.1372	0.1372	0.1379	0.1924	0	1	0.1486	0.1383	0.1118	0.1642	0.1499	0	1	0.0635	0	1	0.2536	0.1111	0.1149	0.0897	0.1171	0.2053	0.1836	0.1015

Malaria

Name	Description	Type	Value
interv	data frame of intervention coverage by year	Dataframe	…
clin_inc	data frame of clinical incidence by age, district, intervention coverage	Dataframe	…
inf_inc	data frame of infection incidence by age, district, intervention coverage	Dataframe	…
sev_inc	data frame of severe case incidence by age, district, intervention coverage	Dataframe	…
itn_district	data frame of ITN usage rates by district	Dataframe	…
irs_district	data frame of IRS usage rates by district	Dataframe	…
sev_symp_prob	probabilities of each symptom for severe malaria cases	Dataframe	…
sensitivity_rdt	Sensitivity of rdt	Real	0.95
cfr	case-fatality rate for severe malaria	Real	0.15
dur_asym	duration (days) of asymptomatic malaria	Real	110.0
dur_clin	duration (days) of clinical symptoms of malaria	Real	5.0
dur_clin_para	duration (days) of parasitaemia for clinical malaria cases	Real	195.0
treatment_adjustment	probability of death from severe malaria if on treatment	Real	0.5
p_sev_anaemia_preg	probability of severe anaemia in pregnant women with clinical malaria	Real	0.075
mortality_adjust	adjustment of case-fatality rate to match WHO/MAP	Real	10.0
data_end	final year of ICL malaria model outputs, after 2018 = projections	Real	2018.0
irs_rates_boundary	threshold for indoor residual spraying coverage	Real	0.5
irs_rates_upper	indoor residual spraying high coverage	Real	0.8
irs_rates_lower	indoor residual spraying low coverage	Real	0.0
prob_malaria_case_tests	probability that a malaria case will have a scheduled rdt	Real	0.4
itn	projected future itn coverage	Real	0.6
rdt_testing_rates	per capita rdt testing rate of general population	Dataframe	…
scaling_factor_for_rdt_availability	scaling factor applied to the reports of rdt usage to compensate fornon-availability of rdts at some facilities	Real	1.2
duration_iptp_protection_weeks	duration of protection against clinical malaria conferred by each dose of IPTp	Real	6.0
rr_clinical_malaria_hiv_under5	relative risk of clinical malaria if HIV+ and aged under 5 years	Real	1.7
rr_clinical_malaria_hiv_over5	relative risk of clinical malaria if HIV+ and aged over 5 years	Real	2.6
rr_clinical_malaria_hiv_pregnant	relative risk of clinical malaria if HIV+ and pregnant	Real	3.96
rr_clinical_malaria_cotrimoxazole	relative risk of clinical malaria if on cotrimoxazole	Real	0.58
rr_clinical_malaria_art	relative risk of clinical malaria if HIV+ and on ART and virally suppressed	Real	0.74
rr_clinical_malaria_iptp	relative risk of clinical malaria with each dose of IPTp	Real	0.54
rr_severe_malaria_hiv_under5	relative risk of severe malaria if HIV+ and aged under 5 years	Real	9.69
rr_severe_malaria_hiv_over5	relative risk of severe malaria if HIV+ and aged over 5 years	Real	2.68
rr_severe_malaria_hiv_pregnant	relative risk of clinical malaria if HIV+ and pregnant	Real	2.8
rr_severe_malaria_iptp	relative risk of severe malaria with each dose of IPTp	Real	0.6
prob_of_treatment_success	probability that treatment will clear malaria symptoms	Real	1.0
type_of_scaleup	argument to determine type scale-up of program which will be implemented, can be ‘none’, ‘target’ or ‘max’	String	none
scaleup_start_year	the year when the scale-up starts (it will occur on 1st January of that year)	Integer	2025
scaleup_parameters	the parameters and values changed in scenario analysis	Dataframe	…

interv

Year	ITN_coverage	IRS_coverage	ACT_coverage	MIS_sleptUnderITN	MIS_IPTp_1dose	MIS_IPTp_2dose	MIS_IPTp_3dose
2001	0	0	0	nan	nan	nan	nan
2002	0	0	0	nan	nan	nan	nan
2003	0.0337	0	0	0.02022	nan	nan	nan
2004	0.1149	0	0.011	0.06894	nan	nan	nan
2005	0.2636	0	0.0269	0.15816	nan	nan	nan
2006	0.2405	0	0.0538	0.1443	nan	nan	nan
2007	0.2865	0.00712375	0.0898	0.1719	nan	nan	nan
2008	0.3185	0.00698449	0.1382	0.1911	nan	nan	nan
2009	0.2908	0.0198598	0.2082	0.17448	nan	nan	nan

Only first 10 rows of 26 are shown.

clin_inc

Unnamed: 0	admin	llin	irs	month	inc_age_gp	clin_incidence	age	monthly_inc_clin	monthly_prob_clin
1	Balaka	0.1	0.8	2	clin_inc_0_0.5	0.616651	0	0.0513875	0.0500895
2	Balaka	0.1	0.8	3	clin_inc_0_0.5	0.724266	0	0.0603555	0.0585702
3	Balaka	0.1	0.8	4	clin_inc_0_0.5	0.487449	0	0.0406208	0.0398068
4	Balaka	0.1	0.8	5	clin_inc_0_0.5	0.221309	0	0.0184424	0.0182734
5	Balaka	0.1	0.8	6	clin_inc_0_0.5	0.0654417	0	0.00545347	0.00543863
6	Balaka	0.1	0.8	7	clin_inc_0_0.5	0.00924685	0	0.000770571	0.000770274
7	Balaka	0.1	0.8	8	clin_inc_0_0.5	0.0258359	0	0.00215299	0.00215068
8	Balaka	0.1	0.8	9	clin_inc_0_0.5	0.0592395	0	0.00493663	0.00492446
9	Balaka	0.1	0.8	10	clin_inc_0_0.5	0.0234651	0	0.00195542	0.00195351

Only first 10 rows of 497664 are shown.

inf_inc

Unnamed: 0	admin	llin	irs	month	inf_inc_age_gp	inf_incidence	age	monthly_inc_inf	monthly_prob_inf
1	Balaka	0.1	0.8	2	inf_inc_0_0.5	1.19984	0	0.0999865	0.0951504
2	Balaka	0.1	0.8	3	inf_inc_0_0.5	1.42709	0	0.118924	0.112125
3	Balaka	0.1	0.8	4	inf_inc_0_0.5	0.955087	0	0.0795906	0.0765057
4	Balaka	0.1	0.8	5	inf_inc_0_0.5	0.464054	0	0.0386712	0.037933
5	Balaka	0.1	0.8	6	inf_inc_0_0.5	0.122824	0	0.0102353	0.0101831
6	Balaka	0.1	0.8	7	inf_inc_0_0.5	0.0174689	0	0.00145575	0.00145469
7	Balaka	0.1	0.8	8	inf_inc_0_0.5	0.0559292	0	0.00466077	0.00464993
8	Balaka	0.1	0.8	9	inf_inc_0_0.5	0.110247	0	0.00918724	0.00914517
9	Balaka	0.1	0.8	10	inf_inc_0_0.5	0.0416001	0	0.00346667	0.00346067

Only first 10 rows of 497664 are shown.

sev_inc

Unnamed: 0	admin	llin	irs	month	sev_inc_age_gp	sev_incidence	age	monthly_inc_sev	monthly_prob_sev
1	Balaka	0.1	0.8	2	sev_inc_0_0.5	0.039965	0	0.00333041	0.00332487
2	Balaka	0.1	0.8	3	sev_inc_0_0.5	0.0449733	0	0.00374778	0.00374076
3	Balaka	0.1	0.8	4	sev_inc_0_0.5	0.0293607	0	0.00244672	0.00244373
4	Balaka	0.1	0.8	5	sev_inc_0_0.5	0.0133483	0	0.00111236	0.00111174
5	Balaka	0.1	0.8	6	sev_inc_0_0.5	0.00411232	0	0.000342693	0.000342634
6	Balaka	0.1	0.8	7	sev_inc_0_0.5	0.000551552	0	4.59627e-05	4.59616e-05
7	Balaka	0.1	0.8	8	sev_inc_0_0.5	0.00155992	0	0.000129993	0.000129985
8	Balaka	0.1	0.8	9	sev_inc_0_0.5	0.00409992	0	0.00034166	0.000341602
9	Balaka	0.1	0.8	10	sev_inc_0_0.5	0.00162945	0	0.000135787	0.000135778

Only first 10 rows of 497664 are shown.

itn_district

District	Year	itn_rate
Balaka	2011	0.3
Balaka	2012	0.5
Balaka	2013	0.7
Balaka	2014	0.6
Balaka	2015	0.4
Balaka	2016	0.6
Balaka	2017	0.6
Balaka	2018	0.6
Blantyre	2010	0.5

Only first 10 rows of 288 are shown.

irs_district

District	Year	irs_rate
Balaka	2011	0
Balaka	2012	0
Balaka	2013	0
Balaka	2014	0
Balaka	2015	0
Balaka	2016	0
Balaka	2017	0
Balaka	2018	0
Blantyre	2010	0

Only first 10 rows of 288 are shown.

sev_symp_prob

symptom	age_group	prop_lower	prop_upper
acidosis	0_5	0.4	0.45
coma_convulsions	0_5	0.3	0.4
renal_failure	0_5	0.05	0.15
severe_anaemia	0_5	0.4	0.5
shock	0_5	0.05	0.15
jaundice	5_60	0.1	0.6
acidosis	5_60	0.45	0.6
coma_convulsions	5_60	0.38	0.45
renal_failure	5_60	0.1	0.5

Only first 10 rows of 12 are shown.

rdt_testing_rates

Year	NumSuspectedCasesTestedByRDT	NumPositiveCasesTestedByRDT	NumSuspectedCasesTestedByMicroscopy	NumPositiveCasesTestedByMicroscopy	NumTreated	NumMalariaCases	TreatmentCoverage	Population	Rate_rdt_testing
2011	580708	253973	166959	50526	nan	5.46033e+06	nan	1.51461e+07	0.0383404
2012	2.76399e+06	1.28185e+06	103754	283138	nan	4.92953e+06	nan	1.55813e+07	0.177392
2013	3.02902e+06	1.23639e+06	129575	44501	nan	4.5475e+06	nan	1.60248e+07	0.189021
2014	5.34472e+06	2.82768e+06	127752	77635	nan	4.26516e+06	nan	1.6478e+07	0.324356
2015	7.03008e+06	3.58532e+06	240212	75923	nan	4.03294e+06	nan	1.69389e+07	0.415025
2016	8.66124e+06	4.73084e+06	216643	96538	nan	3.86857e+06	nan	1.74056e+07	0.497611
2017	9.41394e+06	4.90134e+06	198534	46099	nan	3.85109e+06	nan	1.78812e+07	0.526473
2018	1.13841e+07	5.83074e+06	132475	34735	7.04301e+06	3.78227e+06	1.86211	1.83679e+07	0.619783
2019	1.08613e+07	5.15378e+06	406907	30328	5.08972e+06	3.83515e+06	1.32712	1.88673e+07	0.575668

Only first 10 rows of 15 are shown.

scaleup_parameters

parameter	target_value	min_value	max_value
prob_malaria_case_tests	1	0	1
rdt_testing_rates	0.8	0	1
prob_of_treatment_success	1	0	1
irs_district	0.8	0	0.8
itn_district	0.7	0	0.7
itn	0.7	0	0.7

Measles

Name	Description	Type	Value
beta_baseline	Baseline measles transmission probability	Real	0.00216
beta_scale	Scale value for measles transmission probability sinusoidal function	Real	1.0
phase_shift	Phase shift for measles transmission probability sinusoidal function	Real	5.0
period	Period for measles transmission probability sinusoidal function	Real	12.0
vaccine_efficacy_1	Efficacy of first measles vaccine dose against measles infection	Real	0.85
vaccine_efficacy_2	Efficacy of second measles vaccine dose against measles infection	Real	0.99
prob_severe	Probability of severe measles infection, requiring hospitalisation	Real	0.05
risk_death_on_treatment	Risk of scheduled death occurring if on treatment for measles complications	Real	0.38
symptom_prob	Probability of each symptom with measles infection	Dataframe	…
case_fatality_rate	Probability that case of measles will result in death if not treated	Dictionary	…

symptom_prob

age	symptom	probability
1	rash	1
2	rash	1
3	rash	1
4	rash	1
5	rash	1
6	rash	1
7	rash	1
8	rash	1
9	rash	1

Only first 10 rows of 217 are shown.

case_fatality_rate

0	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30
0.03	0.03	0.03	0.03	0.03	0.01	0.01	0.01	0.01	0.01	0.00333333	0.00333333	0.00333333	0.00333333	0.00333333	0.00333333	0.00333333	0.00333333	0.00333333	0.00333333	0.00333333	0.00333333	0.00333333	0.00333333	0.00333333	0.00333333	0.00333333	0.00333333	0.00333333	0.00333333	0.00333333

NewbornOutcomes

Name	Description	Type	Value
prob_care_seeking_for_complication	baseline probability that a mother will seek care for an unwell neonate following delivery	List	[0.782, 0.782]
prob_day_reaches_week_one_event	Probabilities for day of attendance at postnatal week one event	List	[[0.4, 0.3, 0.2, 0.05, 0.05], [0.4, 0.3, 0.2, 0.05, 0.05]]
prob_early_onset_neonatal_sepsis_day_0	baseline probability of a neonate developing early onset sepsis between birth and 24hrs	List	[0.02, 0.017]
rr_eons_maternal_chorio	relative risk of EONS in newborns whose mothers have chorioamnionitis	List	[6.6, 6.6]
rr_eons_maternal_prom	relative risk of EONS in newborns whose mothers have PROM	List	[4.9, 4.9]
rr_eons_preterm_neonate	relative risk of EONS in preterm newborns	List	[3.36, 3.36]
cfr_early_onset_sepsis	case fatality rate for a neonate due to neonatal sepsis	List	[0.064, 0.056]
cfr_late_onset_sepsis	case fatality rate for a neonate due to neonatal sepsis	List	[0.064, 0.056]
prob_mild_impairment_post_sepsis	probability of the mild neurodevelopmental impairment in survivors of sepsis	List	[0.12, 0.12]
prob_mod_severe_impairment_post_sepsis	probability of the moderate or severe neurodevelopmental impairment in survivors of sepsis	List	[0.23, 0.23]
prob_failure_to_transition	baseline probability of a neonate developing intrapartum related complications (previously birth asphyxia) following delivery	List	[0.01, 0.01]
prob_enceph_no_resus	Probability of a newborn who was not breathing at birth, and didnt receive resuscitation, developing encephalopathy	List	[0.5, 0.5]
cfr_failed_to_transition	case fatality rate for a neonate following failure to transition	List	[0.2, 0.2]
prob_encephalopathy	baseline odds of a neonate developing encephalopathy of any severity following birth	List	[0.0097, 0.0097]
rr_enceph_neonatal_sepsis	relative risk of neonatal encephalopathy if the neonate is also septic	List	[8.67, 8.67]
rr_enceph_obstructed_labour	relative risk for encephalopathy if the mothers labour was obstructed	List	[3.8, 3.8]
rr_enceph_acute_hypoxic_event	relative risk for encephalopathy if the mothers experience an acute event in labour	List	[8.74, 8.74]
prob_enceph_severity	probability of the severity of encephalopathy in a newborn who is encephalopathic	List	[[0.422, 0.338, 0.24], [0.422, 0.338, 0.24]]
prob_mild_impairment_post_enceph	probability of the mild neurodevelopmental impairment in survivors of encephalopathy	List	[0.21, 0.21]
prob_mod_severe_impairment_post_enceph	probability of the moderate or severe neurodevelopmental impairment in survivors of encephalopathy	List	[0.269, 0.269]
cfr_enceph	case fatality rate for a neonate due to mild encephalopathy	List	[0.48, 0.28]
cfr_multiplier_severe_enceph	multiplier for risk of death in a neonate with severe encephalopathy	List	[1.91, 3.28]
prob_respiratory_distress_preterm	probability that a preterm infant will experience respiratory distress at birth	List	[0.12, 0.12]
rr_rds_early_preterm	relative risk of RDS in a preterm newborn born before 34 weeks	List	[2.64, 2.64]
rr_rds_maternal_diabetes_mellitus	relative risk of RDS in a preterm newborn whose mother has DM	List	[2.66, 2.66]
rr_rds_maternal_gestational_diab	relative risk of RDS in a preterm newborn whose mother has gestational diabetes	List	[1.57, 1.57]
cfr_respiratory_distress_syndrome	case fatality rate for respiratory distress syndrome of prematurity	List	[0.29, 0.2]
prob_mild_disability_preterm_<32weeks	probability of mild long term neurodevelopmental disability in preterm infants born at less than 32 weeks gestation	List	[0.324, 0.324]
prob_mod_severe_disability_preterm_<32weeks	probability of moderate/severe longterm neurodevelopmental disability in preterm infants born at less than 32 weeks gestation	List	[0.246, 0.246]
prob_mild_disability_preterm_32_36weeks	probability of mild long term neurodevelopmental disability in preterm infants born between 32 and 36 weeks gestation	List	[0.034, 0.034]
prob_mod_severe_disability_preterm_32_36weeks	probability of moderate/severe long term neurodevelopmental disability in preterm infants born between 32 and 36 weeks gestation	List	[0.018, 0.018]
prob_retinopathy_preterm_early	Probability that a neonate born at less than 32 weeks who survives the neonatal period will develop retinopathy	List	[0.365, 0.365]
prob_retinopathy_preterm_late	Probability that a neonate born at less than 32 weeks who survives the neonatal period will develop retinopathy	List	[0.077, 0.077]
prob_retinopathy_severity_no_treatment	Probabilities that a preterm neonate who developed retinopathy will experience the following vision impairments: none, mild, moderate or blindness	List	[[0.28, 0.03, 0.1, 0.12, 0.47], [0.28, 0.03, 0.1, 0.12, 0.47]]
cfr_preterm_birth	case fatality rate for a neonate born prematurely	List	[0.0227, 0.0187]
rr_preterm_death_early_preterm	relative risk of preterm death in early preterm neonates	List	[1.66, 1.66]
prob_preterm_death_by_day	probability of death due to preterm complications occurring on days 0-14	List	[[0.4, 0.2, 0.15, 0.05, 0.02, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018], [0.4, 0.2, 0.15, 0.05, 0.02, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018, 0.018]]
prob_congenital_heart_anomaly	Probability of a congenital heart anomaly in the newborn	List	[0.009, 0.009]
prob_limb_musc_skeletal_anomaly	Probability of a congenital limb or musculoskeletal anomaly in the newborn	List	[0.008, 0.008]
prob_urogenital_anomaly	Probability of a congenital urogenital anomaly in the newborn	List	[0.003, 0.003]
prob_digestive_anomaly	Probability of a congenital digestive anomaly in the newborn	List	[0.0007, 0.0007]
prob_other_anomaly	Probability of a other congenital anomalies in the newborn	List	[0.0004, 0.0004]
cfr_congenital_heart_anomaly	case fatality rate for newborns with congenital heart anomalies	List	[0.062, 0.062]
cfr_limb_or_musculoskeletal_anomaly	case fatality rate for newborns with congenital limb/musculoskeletal anomalies	List	[0.0069, 0.0069]
cfr_urogenital_anomaly	case fatality rate for newborns with congenital urogenital anomalies	List	[0.0085, 0.0085]
cfr_digestive_anomaly	case fatality rate for newborns with congenital digestive anomalies	List	[0.2829, 0.2829]
cfr_other_anomaly	case fatality rate for newborns with other congenital anomalies	List	[0.131, 0.131]
prob_cba_death_by_age_group	probabilities that death from a congenital birth anomaly will occur once the individual reaches the following age groups: early neonatal, late neonatal, post neonatal 1-4 years, 5-9 years, 10 -14 years or 15-69 years	List	[[0.27, 0.08, 0.38, 0.2, 0.02, 0.01, 0.04], [0.3, 0.09, 0.35, 0.18, 0.03, 0.02, 0.03]]
prob_early_breastfeeding_hb	probability that a neonate will be breastfed within the first hour following birth when delivered at home	List	[0.94, 0.67]
prob_breastfeeding_type	probabilities that a woman is 1.) not breastfeeding 2.) non-exclusively breastfeeding 3.)exclusively breastfeeding at birth (until 6 months)	List	[[0.005, 0.277, 0.718], [0.101, 0.289, 0.61]]
prob_early_breastfeeding_hf	probability that a neonate will be breastfed within the first hour following birth when delivered at a health facility	List	[0.94, 0.77]
prob_pnc_check_newborn	probability that a neonate will receive a full postnatal check	List	[0.6, 0.6]
prob_timings_pnc_newborns	probabilities that a postnatal check will happen before or after 48 hours alive	List	[[0.97, 0.03], [0.97, 0.03]]
prob_kmc_available	probability that KMC can be delivered in a given hospital	List	[0.62, 0.62]
treatment_effect_inj_abx_sep	effect of injectable antibiotics treatment on reducing mortality from sepsis	List	[0.35, 0.35]
treatment_effect_supp_care_sep	effect of full supportive care treatment on reducing mortality from sepsis	List	[0.2, 0.2]
treatment_effect_cord_care	effect of full supportive care treatment on reducing incidence of sepsis	List	[0.77, 0.77]
treatment_effect_clean_birth	effect of clean birth practices on reducing incidence of sepsis	List	[0.73, 0.73]
treatment_effect_early_init_bf	effect of early initiation of breastfeeding on reducing incidence of sepsis	List	[0.55, 0.55]
treatment_effect_resuscitation	effect of resuscitation on newborn mortality associated with encephalopathy	List	[0.63, 0.63]
treatment_effect_resuscitation_preterm	effect of resuscitation on newborn mortality associated with prematurity	List	[0.81, 0.81]
treatment_effect_abx_prom	effect of antibiotics given to mothers experience PROM on risk of newborn sepsis	List	[0.67, 0.67]
treatment_effect_steroid_preterm	relative risk of death for preterm neonates following administration of antenatal corticosteroids	List	[0.71, 0.71]
treatment_effect_kmc	treatment effect of kangaroo mother care on preterm mortality	List	[0.49, 0.49]

OesophagealCancer

Name	Description	Type	Value
init_prop_oes_cancer_stage	initial proportions in dysplasia/cancer categories for man aged 20 with no excess alcohol and no tobacco	List	[0.0003, 0.0001, 5e-06, 3e-05, 5e-05, 1e-05]
init_prop_dysphagia_oes_cancer_by_stage	initial proportions of those with dysplasia/cancer categories that have the symptom dysphagia	List	[0.01, 0.03, 0.1, 0.2, 0.3, 0.8]
init_prop_with_dysphagia_diagnosed_oes_cancer_by_stage	initial proportions of people that have symptom of dysphagia that have been diagnosed	List	[0.8, 0.85, 0.9, 0.95, 0.98, 0.9]
init_prop_treatment_status_oes_cancer	initial proportions of people with oesophageal dysplasia/cancer that had initiated treatment	List	[0.01, 0.01, 0.05, 0.05, 0.05, 0.05]
init_prob_palliative_care	initial probability of being under palliative care if in stage 4	Real	0.5
r_low_grade_dysplasia_none	probabilty per 3 months of incident low grade oesophageal dysplasia, amongst people with no oesophageal dysplasia (men, age20, no excess alcohol, no tobacco)	Real	5e-07
rr_low_grade_dysplasia_none_female	rate ratio for low grade oesophageal dysplasia for females	Real	1.3
rr_low_grade_dysplasia_none_per_year_older	rate ratio for low grade oesophageal dysplasia per year older from age 20	Real	1.1
rr_low_grade_dysplasia_none_tobacco	rate ratio for low grade oesophageal dysplasia for tobacco smokers	Real	2.0
rr_low_grade_dysplasia_none_ex_alc	rate ratio for low grade oesophageal dysplasia for no excess alcohol	Real	1.0
r_high_grade_dysplasia_low_grade_dysp	probabilty per 3 months of high grade oesophageal dysplasia, amongst people with low grade dysplasia	Real	0.03
rr_high_grade_dysp_undergone_curative_treatment	rate ratio for high grade dysplasia for people with low grade dysplasia if had curative treatment at low grade dysplasia stage	Real	0.1
r_stage1_high_grade_dysp	probabilty per 3 months of stage 1 oesophageal cancer amongst people with high grade dysplasia	Real	0.01
rr_stage1_undergone_curative_treatment	rate ratio for stage 1 oesophageal cancer for people with high grade dysplasia if had curative treatment at high grade dysplasia stage	Real	0.1
r_stage2_stage1	probabilty per 3 months of stage 2 oesophageal cancer amongst people with stage 1	Real	0.05
rr_stage2_undergone_curative_treatment	rate ratio for stage 2 oesophageal cancer for people with stage 1 oesophageal cancer if had curative treatment at stage 1	Real	0.1
r_stage3_stage2	probabilty per 3 months of stage 3 oesophageal cancer amongst people with stage 2	Real	0.05
rr_stage3_undergone_curative_treatment	rate ratio for stage 3 oesophageal cancer for people with stage 2 oesophageal cancer if had curative treatment at stage 2	Real	0.1
r_stage4_stage3	probabilty per 3 months of stage 4 oesophageal cancer amongst people with stage 3	Real	0.05
rr_stage4_undergone_curative_treatment	rate ratio for stage 4 oesophageal cancer for people with stage 3 oesophageal cancer if had curative treatment at stage 3	Real	0.3
rate_palliative_care_stage4	prob palliative care this 3 month period if stage4	Real	0.5
r_death_oesoph_cancer	probabilty per 3 months of death from oesophageal cancer mongst people with stage 4 oesophageal cancer	Real	0.4
rr_dysphagia_low_grade_dysp	probability per 3 months of dysphagia in a person with low grade oesophageal dysplasia	Real	1.0
rr_dysphagia_high_grade_dysp	rate ratio for dysphagia if have high grade oesophageal dysplasia	Real	1.0
r_dysphagia_stage1	rate ratio for dysphagia if have stage 1 oesophageal cancer	Real	0.01
rr_dysphagia_stage2	rate ratio for dysphagia if have stage 2 oesophageal cancer	Real	2.0
rr_dysphagia_stage3	rate ratio for dysphagia if have stage 3 oesophageal cancer	Real	50.0
rr_dysphagia_stage4	rate ratio for dysphagia if have stage 4 oesophageal cancer	Real	100.0
rp_oes_cancer_female	relative prevalence at baseline of oesophageal dysplasia/cancer if female	Real	1.3
rp_oes_cancer_per_year_older	relative prevalence at baseline of oesophageal dysplasia/cancer per year older than 20	Real	1.1
rp_oes_cancer_tobacco	relative prevalence at baseline of oesophageal dysplasia/cancer if tobacco	Real	2.0
rp_oes_cancer_ex_alc	relative prevalence at baseline of oesophageal dysplasia/cancer	Real	1.0
sensitivity_of_endoscopy_for_oes_cancer_with_dysphagia	sensitivity of endoscopy_for diagnosis of oesophageal cancer for those with dysphagia	Real	1.0

OtherAdultCancer

Name	Description	Type	Value
init_prop_early_other_adult_ca_symptom_other_adult_cancer_by_stage	initial proportions of those with other adult cancer categories that have other adult_ca_symptom	List	[0.3, 0.5, 0.8]
in_prop_other_adult_cancer_stage	initial proportions in other adult cancer stages for person aged 15-29	List	[0.0002, 0.0002, 0.0004]
init_prop_with_early_other_adult_ca_symptom_diagnosed_by_stage	initial proportions of people that have symptom of other_adult_ca_symptom that have been diagnosed	List	[0.3, 0.4, 0.5]
init_prop_treatment_status_other_adult_cancer	initial proportions of people with other_adult cancer previously given treatment	List	[0.1, 0.1, 0.1]
init_prob_palliative_care	initial probability of being under palliative care if in metastatic	Real	0.95
r_site_confined_none	probabilty per 3 months of incident site_confined other_adult cancer amongst people age 15-29 with no other adult cancer	Real	1e-05
rr_site_confined_age3049	rate ratio for site-confined other_adult cancer for age 30-49	Real	5.0
rr_site_confined_age5069	rate ratio for site-confined other_adult cancer for age 50-69	Real	21.0
rr_site_confined_agege70	rate ratio for site-confined other_adult cancer for age ge 70	Real	60.0
rr_site_confined_hiv	rate ratio for site-confined other_adult_cancer if infected with HIV	Real	4.13
r_local_ln_site_confined_other_adult_ca	probabilty per 3 months of local ln other_adult cancer amongst people with site confined	Real	0.15
rr_local_ln_other_adult_ca_undergone_curative_treatment	rate ratio for local_ln for people with site_confined if had curative treatment at site_confined stage	Real	0.1
r_metastatic_local_ln	probabilty per 3 months of metastatic other_adult cancer amongst people with local_ln	Real	0.15
rr_metastatic_undergone_curative_treatment	rate ratio for metastatic Other_adult cancer for people with local_lnOther_adult cancer if had curative treatment at local_ln	Real	0.2
r_death_other_adult_cancer	probabilty per 3 months of death from other adult cancer mongst people with metastatic other_adult cancer	Real	0.2
r_early_other_adult_ca_symptom_site_confined_other_adult_ca	probability per 3 months of other_adult_ca_symptom in a person with site confined other_adult cancer	Real	0.02
rr_early_other_adult_ca_symptom_local_ln_other_adult_ca	rate ratio for other_adult_ca_symptom if have high grade other_adult cancer	Real	3.0
rr_early_other_adult_ca_symptom_metastatic_other_adult_ca	rate ratio for other_adult_ca_symptom if have metastatic other_adult cancer	Real	10.0
rp_other_adult_cancer_age3049	relative prevalence at baseline of bladder cancer/cancer age 30-49	Real	1.5
rp_other_adult_cancer_age5069	relative prevalence at baseline of bladder cancer/cancer age 50-69	Real	2.0
rp_other_adult_cancer_agege70	relative prevalence at baseline of bladder cancer/cancer age 70+	Real	4.0
sensitivity_of_diagnostic_device_for_other_adult_cancer_with_other_adult_ca_site_confined	sensitivity of diagnostic_device_for diagnosis of other_adult cancer for those with other_adult_ca_site-confined	Real	0.8
sensitivity_of_diagnostic_device_for_other_adult_cancer_with_other_adult_ca_local_ln	sensitivity of diagnostic_device_for diagnosis of other_adult cancer for those with other_adult_local_ln	Real	0.95
sensitivity_of_diagnostic_device_for_other_adult_cancer_with_other_adult_ca_metastatic	sensitivity of diagnostic_device_for diagnosis of other_adult cancer for those with other_adult_ca metastatic	Real	0.95

PostnatalSupervisor

Name	Description	Type	Value
prob_obstetric_fistula	probability of a woman developing an obstetric fistula after birth	List	[0.00426, 0.00426]
rr_obstetric_fistula_obstructed_labour	relative risk of obstetric fistula in women who experienced obstructed labour	List	[14.8, 14.8]
prevalence_type_of_fistula	prevalence of 1.) vesicovaginal 2.)rectovaginal fistula	List	[[0.924, 0.076], [0.924, 0.076]]
prob_secondary_pph	baseline probability of secondary PPH	List	[0.0002, 0.00034]
rr_secondary_pph_endometritis	relative risk of secondary postpartum haemorrhage in women with sepsis secondary to endometritis	List	[1, 1]
prob_secondary_pph_severity	probability of mild, moderate or severe secondary PPH	List	[[0.33, 0.33, 0.34], [0.33, 0.33, 0.34]]
cfr_secondary_postpartum_haemorrhage	case fatality rate for secondary pph	List	[0.22, 0.08]
prob_htn_resolves	Weekly probability of resolution of hypertension	List	[0.167, 0.167]
weekly_prob_gest_htn_pn	weekly probability of a woman developing gestational hypertension during the postnatal period	List	[0.0025, 0.0025]
rr_gest_htn_obesity	Relative risk of gestational hypertension for women who are obese	List	[3.31, 3.31]
weekly_prob_pre_eclampsia_pn	weekly probability of a woman developing mild pre-eclampsia during the postnatal period	List	[0.0017, 0.0017]
rr_pre_eclampsia_obesity	Relative risk of pre-eclampsia for women who are obese	List	[3.2, 3.2]
rr_pre_eclampsia_chronic_htn	Relative risk of pre-eclampsia in women who are chronically hypertensive	List	[2.26, 2.26]
rr_pre_eclampsia_diabetes_mellitus	Relative risk of pre-eclampsia in women who have diabetes mellitus	List	[3.7, 3.7]
probs_for_mgh_matrix_pn	probability of mild gestational hypertension moving between states: gestational hypertension, severe gestational hypertension, mild pre-eclampsia, severe pre-eclampsia, eclampsia	List	[[0.918, 0.032, 0.05, 0, 0], [0.918, 0.032, 0.05, 0, 0]]
probs_for_sgh_matrix_pn	probability of severe gestational hypertension moving between states: gestational hypertension, severe gestational hypertension, mild pre-eclampsia, severe pre-eclampsia, eclampsia	List	[[0, 0.92, 0, 0.08, 0], [0, 0.92, 0, 0.08, 0]]
probs_for_mpe_matrix_pn	probability of mild pre-eclampsia moving between states: gestational hypertension, severe gestational hypertension, mild pre-eclampsia, severe pre-eclampsia, eclampsia	List	[[0, 0, 0.95, 0.05, 0], [0, 0, 0.95, 0.05, 0]]
probs_for_spe_matrix_pn	probability of severe pre-eclampsia moving between states: gestational hypertension, severe gestational hypertension, mild pre-eclampsia, severe pre-eclampsia, eclampsia	List	[[0, 0, 0, 0.95, 0.05], [0, 0, 0, 0.95, 0.05]]
probs_for_ec_matrix_pn	probability of eclampsia moving between states: gestational hypertension, severe gestational hypertension, mild pre-eclampsia, severe pre-eclampsia, eclampsia	List	[[0, 0, 0, 0, 1], [0, 0, 0, 0, 1]]
cfr_eclampsia	case fatality rate of eclampsia in the postnatal period	List	[0.028, 0.03]
cfr_severe_pre_eclampsia	case fatality rate of severe pre-eclampsia in the postnatal period	List	[0.018, 0.018]
weekly_prob_death_severe_gest_htn	weekly risk of death from severe hypertension in the postnatal period	List	[2e-05, 2e-05]
baseline_prob_anaemia_per_week	Weekly probability of anaemia in pregnancy	List	[0.017, 0.024]
rr_anaemia_maternal_malaria	relative risk of anaemia secondary to malaria infection	List	[1.45, 1.45]
rr_anaemia_recent_haemorrhage	relative risk of anaemia secondary to recent haemorrhage	List	[1.93, 1.93]
rr_anaemia_hiv_no_art	relative risk of anaemia for a woman with HIV not on ART	List	[4.19, 4.19]
prob_type_of_anaemia_pn	probability of a woman with anaemia having mild, moderate or severe anaemia	List	[[0.52, 0.475, 0.005], [0.52, 0.475, 0.005]]
prob_late_sepsis_endometritis	probability of developing sepsis following postpartum endometritis infection	List	[6.9e-05, 6.2e-05]
rr_sepsis_endometritis_post_cs	relative risk of endometritis following caesarean delivery	List	[12.1, 12.1]
prob_late_sepsis_urinary_tract	probability of developing sepsis following postpartum UTI	List	[5.4e-05, 5.4e-05]
prob_late_sepsis_skin_soft_tissue	probability of developing sepsis following postpartum skin/soft tissue infection	List	[3.9e-05, 3.5e-05]
rr_sepsis_sst_post_cs	relative risk of skin/soft tissue sepsis following caesarean delivery	List	[3.9, 3.9]
cfr_postpartum_sepsis	case fatality rate for postnatal sepsis	List	[0.75, 0.49]
prob_early_onset_neonatal_sepsis_week_1	Baseline probability of a newborn developing sepsis in week one of life	List	[0.02, 0.017]
rr_eons_maternal_chorio	relative risk of EONS in newborns whose mothers have chorioamnionitis	List	[6.6, 6.6]
rr_eons_maternal_prom	relative risk of EONS in newborns whose mothers have PROM	List	[4.9, 4.9]
rr_eons_preterm_neonate	relative risk of EONS in preterm newborns	List	[3.36, 3.36]
cfr_early_onset_neonatal_sepsis	case fatality for early onset neonatal sepsis	List	[0.064, 0.056]
prob_late_onset_neonatal_sepsis	probability of late onset neonatal sepsis (all cause)	List	[0.0045, 0.0038]
cfr_late_neonatal_sepsis	Risk of death from late neonatal sepsis	List	[0.064, 0.056]
prob_sepsis_disabilities	Probabilities of varying disability levels after neonatal sepsis	List	[[0.4, 0.1, 0.3, 0.1, 0.1], [0.4, 0.1, 0.3, 0.1, 0.1]]
prob_care_seeking_postnatal_emergency	baseline probability of emergency care seeking for women in the postnatal period	List	[0.782, 0.782]
prob_care_seeking_postnatal_emergency_neonate	baseline probability care will be sought for a neonate with a complication	List	[0.782, 0.782]
odds_care_seeking_fistula_repair	odds of a woman seeking care for treatment of obstetric fistula	List	[1.5, 1.5]
aor_cs_fistula_age_15_19	odds ratio for care seeking for treatment of obstetric fistula in 15-19 year olds	List	[0.31, 0.31]
aor_cs_fistula_age_lowest_education	odds ratio for care seeking for treatment of obstetric fistula in women in the lowest education quantile	List	[0.69, 0.69]
treatment_effect_early_init_bf	effect of early initiation of breastfeeding on neonatal sepsis rates	List	[0.55, 0.55]
treatment_effect_iron_folic_acid_anaemia	effect of iron and folic acid supplementation on anaemia risk	List	[0.3, 0.3]
treatment_effect_abx_prom	effect of early antibiotics given to a mother with PROM on neonatal sepsis rates	List	[0.67, 0.67]
treatment_effect_clean_birth	Treatment effect of clean birth practices on early onset neonatal sepsis risk	List	[0.73, 0.73]
treatment_effect_cord_care	Treatment effect of chlorhexidine cord care on early onset neonatal sepsis risk	List	[0.77, 0.77]
treatment_effect_anti_htns_progression_pn	Treatment effect of oral anti hypertensives on progression from mild/mod to severe gestationalhypertension	List	[0.49, 0.49]

PregnancySupervisor

Name	Description	Type	Value
prob_ectopic_pregnancy	probability of ectopic pregnancy	List	[0.01, 0.01]
prob_care_seeking_ectopic_pre_rupture	probability a woman will seek care for ectopic pregnancy prior to rupture	List	[0.08, 0.08]
prob_ectopic_pregnancy_death	probability of a woman dying from a ruptured ectopic pregnancy	List	[0.02, 0.012]
prob_multiples	probability that a woman is currently carrying more than one pregnancy	List	[0.0399, 0.0399]
prob_placenta_praevia	probability that this womans pregnancy will be complicated by placenta praevia	List	[0.005, 0.0058]
rr_placenta_praevia_previous_cs	relative risk of placenta praevia in a woman who has previously delivered via caesarean section	List	[1.47, 1.47]
prob_syphilis_during_pregnancy	probability that this womans will develop syphilis during her pregnancy	List	[0.028, 0.028]
prob_previous_miscarriage_at_baseline	probability that a woman at baseline will have previously experienced a miscarriage	Real	0.047
prob_spontaneous_abortion_per_month	underlying risk of spontaneous abortion per month	List	[[0.025, 0.037, 0.05, 0.037, 0.025], [0.025, 0.037, 0.05, 0.037, 0.025]]
rr_spont_abortion_age_35	relative risk of spontaneous abortion in women aged 35 years or older	List	[4, 4]
rr_spont_abortion_age_31_34	relative risk of spontaneous abortion in women aged 31-34 years old	List	[2.31, 2.31]
rr_spont_abortion_prev_sa	relative risk of spontaneous abortion in women who have previously experiences spontaneous abortion	List	[2.23, 2.23]
prob_complicated_sa	probability that a woman who experiences spontaneous abortion with experience any complications	List	[0.11, 0.11]
prob_induced_abortion_per_month	underlying risk of induced abortion per month	List	[0.038, 0.038]
prob_complicated_ia	probability that a woman who experiences induced abortion with experience any complications	List	[0.37, 0.37]
prob_haemorrhage_post_abortion	probability of haemorrhage following an abortion	List	[0.23, 0.23]
prob_sepsis_post_abortion	probability of sepsis following an abortion	List	[0.137, 0.137]
prob_injury_post_abortion	probability of injury following an abortion	List	[0.056, 0.056]
prob_induced_abortion_death	underlying risk of death following an induced abortion	List	[0.005, 0.0025]
prob_spontaneous_abortion_death	underlying risk of death following an spontaneous abortion	List	[0.01, 0.005]
baseline_prob_anaemia_per_month	baseline risk of a woman developing anaemia secondary only to pregnant	List	[0.1, 0.12]
rr_anaemia_maternal_malaria	relative risk of anaemia secondary to malaria infection	List	[1.45, 1.45]
rr_anaemia_hiv_no_art	relative risk of anaemia for a woman with HIV not on ART	List	[4.19, 4.19]
prob_mild_mod_sev_anaemia	probabilities that a womans anaemia will be mild, moderate or severe	List	[[0.52, 0.475, 0.005], [0.5, 0.46, 0.04]]
prob_gest_diab_per_month	underlying risk of gestational diabetes per month without the impact of risk factors	List	[0.0056, 0.0056]
rr_gest_diab_obesity	Relative risk of gestational diabetes for women who are obese	List	[3.97, 3.97]
prob_gest_htn_per_month	underlying risk of gestational hypertension per month without the impact of risk factors	List	[0.0073, 0.0073]
rr_gest_htn_obesity	Relative risk of gestational hypertension for women who are obese	List	[3.31, 3.31]
prob_pre_eclampsia_per_month	underlying risk of pre-eclampsia per month without the impact of risk factors	List	[0.0065, 0.0065]
rr_pre_eclampsia_obesity	Relative risk of pre-eclampsia for women who are obese	List	[3.2, 3.2]
rr_pre_eclampsia_multiple_pregnancy	Relative risk of pre-eclampsia for women who are pregnant with twins	List	[4.07, 4.07]
rr_pre_eclampsia_chronic_htn	Relative risk of pre-eclampsia in women who are chronically hypertensive	List	[2.26, 2.26]
rr_pre_eclampsia_diabetes_mellitus	Relative risk of pre-eclampsia in women who have diabetes mellitus	List	[3.7, 3.7]
probs_for_mgh_matrix	probability of mild gestational hypertension moving between states: gestational hypertension, severe gestational hypertension, mild pre-eclampsia, severe pre-eclampsia, eclampsia	List	[[0.918, 0.032, 0.05, 0, 0], [0.918, 0.032, 0.05, 0, 0]]
probs_for_sgh_matrix	probability of severe gestational hypertension moving between states: gestational hypertension, severe gestational hypertension, mild pre-eclampsia, severe pre-eclampsia, eclampsia	List	[[0, 0.87, 0, 0.13, 0], [0, 0.87, 0, 0.13, 0]]
probs_for_mpe_matrix	probability of mild pre-eclampsia moving between states: gestational hypertension, severe gestational hypertension, mild pre-eclampsia, severe pre-eclampsia, eclampsia	List	[[0, 0, 0.78, 0.22, 0], [0, 0, 0.78, 0.22, 0]]
probs_for_spe_matrix	probability of severe pre-eclampsia moving between states: gestational hypertension, severe gestational hypertension, mild pre-eclampsia, severe pre-eclampsia, eclampsia	List	[[0, 0, 0, 0.16, 0.84], [0, 0, 0, 0.16, 0.84]]
probs_for_ec_matrix	probability of eclampsia moving between states: gestational hypertension, severe gestational hypertension, mild pre-eclampsia, severe pre-eclampsia, eclampsia	List	[[0, 0, 0, 0, 1], [0, 0, 0, 0, 1]]
prob_severe_pre_eclampsia_death	probability of death for a woman experiencing acute severe pre-eclampsia	List	[0.018, 0.018]
prob_eclampsia_death	probability of death for a woman experiencing eclampsia	List	[0.028, 0.03]
prob_monthly_death_severe_htn	monthly risk of death for a woman with severe hypertension	List	[0.0001, 0.0001]
prob_placental_abruption_per_month	monthly probability that a woman will develop placental abruption	List	[0.0005, 0.0005]
rr_placental_abruption_hypertension	Relative risk of placental abruption in women with hypertension	List	[2.2, 2.2]
rr_placental_abruption_previous_cs	Relative risk of placental abruption in women who delivered previously via caesarean section	List	[1.3, 1.3]
prob_aph_placenta_praevia	risk of antepartum haemorrhage due to ongoing placenta praevia	List	[0.09, 0.09]
prob_aph_placental_abruption	risk of antepartum haemorrhage due to placental abruption	List	[0.9, 0.9]
prob_mod_sev_aph	probabilities that APH is mild/moderate or severe	List	[[0.8, 0.2], [0.8, 0.2]]
prob_antepartum_haemorrhage_death	probability of death for a woman suffering acute antepartum haemorrhage	List	[0.11, 0.04]
prob_prom_per_month	monthly probability that a woman will experience premature rupture of membranes	List	[0.0064, 0.0064]
prob_chorioamnionitis	monthly probability of a women developing chorioamnionitis	List	[0.015, 0.013]
prob_antenatal_sepsis_death	case fatality rate for chorioamnionitis	List	[0.75, 0.49]
baseline_prob_early_labour_onset	monthly baseline risk of labour onsetting before term	List	[[0.0008, 0.0033, 0.017, 0.04], [0.0008, 0.0033, 0.017, 0.04]]
rr_preterm_labour_post_prom	relative risk of early labour onset following PROM	List	[5.9, 5.9]
rr_preterm_labour_anaemia	relative risk of early labour onset in women with anaemia	List	[4.58, 4.58]
rr_preterm_labour_malaria	relative risk of early labour onset in women with malaria	List	[3.08, 3.08]
rr_preterm_labour_multiple_pregnancy	relative risk of early labour onset in women pregnant with twins	List	[3.44, 3.44]
prob_still_birth_per_month	underlying risk of stillbirth per month without the impact of risk factors	List	[0.0031, 0.0026]
rr_still_birth_ga_41	relative risk of still birth in women with gestational age 41 weeks	List	[2.24, 2.24]
rr_still_birth_ga_42	relative risk of still birth in women with gestational age 42 weeks	List	[3.88, 3.88]
rr_still_birth_ga_>42	relative risk of still birth in women with gestational age > 42 weeks	List	[6.94, 6.94]
rr_still_birth_gest_diab	relative risk of still birth in women with gestational diabetes	List	[3.91, 3.91]
rr_still_birth_diab_mellitus	relative risk of still birth in women with diabetes mellitus	List	[3.52, 3.52]
rr_still_birth_maternal_malaria	relative risk of still birth in women with malaria	List	[1.81, 1.81]
rr_still_birth_maternal_syphilis	relative risk of still birth in women with syphilis	List	[6.87, 6.87]
rr_still_birth_pre_eclampsia	relative risk of still birth in women with pre-eclampsia	List	[4.15, 4.15]
rr_still_birth_eclampsia	relative risk of still birth in women with eclampsia	List	[4.15, 4.15]
rr_still_birth_gest_htn	relative risk of still birth in women with mild gestational hypertension	List	[1.21, 1.21]
rr_still_birth_chronic_htn	relative risk of still birth in women with chronic hypertension	List	[2.32, 2.23]
rr_still_birth_aph	relative risk of still birth in women with antepartum haemorrhage	List	[2.1, 2.1]
rr_still_birth_chorio	relative risk of still birth in women with chorioamnionitis	List	[2, 2]
prob_seek_care_pregnancy_complication	Probability that a woman who is pregnant will seek care in the event of a complication	List	[0.782, 0.782]
prob_seek_care_pregnancy_loss	Probability that a woman who has developed complications post pregnancy loss will seek care	List	[0.782, 0.782]
prob_seek_care_induction	Probability that a woman who is post term will seek care for induction of labour	List	[0.2, 0.2]
prob_anc1_months_2_to_4	list of probabilities that a woman will attend her first ANC visit at either month 2, 3 or 4 of pregnancy	List	[[0.165, 0.165, 0.67], [0.165, 0.364, 0.471]]
prob_anc1_months_5_to_9	list of probabilities that a woman will attend her first ANC visit on months 5-10	List	[[0.345, 0.245, 0.28, 0.015, 0.015, 0.1], [0.41, 0.25, 0.21, 0.015, 0.015, 0.1]]
odds_early_init_anc4	probability of a woman undergoing 4 or more basic ANC visits with the first visit occurring prior or during month 4 of pregnancy (EANC4+)	List	[0.32, 0.58]
aor_early_anc4_20_24	adjusted odds ratio of EANC4+ in women aged 20-24	List	[1.26, 1.26]
aor_early_anc4_25_29	adjusted odds ratio of EANC4+ in women aged 25-29	List	[1.44, 1.44]
aor_early_anc4_30_34	adjusted odds ratio of EANC4+ in women aged 30-34	List	[1.49, 1.49]
aor_early_anc4_35_39	adjusted odds ratio of EANC4+ in women aged 35-39	List	[1.64, 1.64]
aor_early_anc4_40_44	adjusted odds ratio of EANC4+ in women aged 40-44	List	[1.51, 1.51]
aor_early_anc4_45_49	adjusted odds ratio of EANC4+ in women aged 45-49	List	[1.91, 1.91]
aor_early_anc4_2010	adjusted odds ratio of EANC4+ in 2010	List	[1.51, 1.51]
aor_early_anc4_2015	adjusted odds ratio of EANC4+ in 2015	List	[2.03, 2.03]
aor_early_anc4_parity_2_3	adjusted odds ratio of EANC4+ in women with a parity of 2-3	List	[0.74, 0.74]
aor_early_anc4_parity_4_5	adjusted odds ratio of EANC4+ in women with a parity of 4-5	List	[0.65, 0.65]
aor_early_anc4_parity_6+	adjusted odds ratio of EANC4+ in women with a parity of 6+	List	[0.61, 0.61]
aor_early_anc4_secondary_edu	adjusted odds ratio of EANC4+ in women with secondary education	List	[1.24, 1.24]
aor_early_anc4_tertiary_edu	adjusted odds ratio of EANC4+ in women with tertiary education	List	[2.64, 2.64]
aor_early_anc4_richest_wealth	adjusted odds ratio of EANC4+ in women in the richest wealth quintile	List	[1.32, 1.32]
prob_late_initiation_anc4	probability a woman will undertake 4 or more ANC visits with the first being after 4 months	List	[0.3, 0.29]
prob_early_initiation_anc_below4	probabilities a woman will attend fewer than 4 ANC visits but the first visit will occur before month 4	List	[0.115, 0.101]
prob_early_anc_at_facility_level_1_2	probabilities a woman will attend ANC 1 at facility levels 1 or 2	List	[[0.5, 0.5], [0.5, 0.5]]
treatment_effect_ectopic_pregnancy_treatment	Treatment effect of ectopic pregnancy case management	List	[0.1, 0.1]
treatment_effect_post_abortion_care	Treatment effect of post abortion care	List	[0.2, 0.2]
treatment_effect_iron_folic_acid_anaemia	relative effect of daily iron and folic acid treatment on risk of maternal anaemia	List	[0.3, 0.3]
treatment_effect_calcium_pre_eclamp	risk reduction of pre-eclampsia for women taking daily calcium supplementation	List	[0.45, 0.45]
treatment_effect_gest_htn_calcium	Effect of calcium supplementation on risk of developing gestational hypertension	List	[0.65, 0.65]
treatment_effect_anti_htns_progression	Effect of anti hypertensive medication in reducing the risk of progression from mild to severe hypertension	List	[0.49, 0.49]
prob_glycaemic_control_diet_exercise	probability a womans GDM is controlled by diet and exercise during the first month of treatment	List	[0.5, 0.5]
prob_glycaemic_control_orals	probability a womans GDM is controlled by oral anti-diabetics during the first month of treatment	List	[0.936, 0.936]
treatment_effect_gdm_case_management	Treatment effect of GDM case management on mothers risk of stillbirth	List	[0.9, 0.9]
treatment_effect_still_birth_food_sups	risk reduction of still birth for women receiving nutritional supplements	List	[0.6, 0.6]
anc_service_structure	stores type of ANC service being delivered in the model (anc4 or anc8) and is used in analysisscripts to change ANC structure	Integer	8
analysis_year	Year on which the pregnancy analysis event is scheduled to update any relevant parameters for analysis (1st day 1st month)	Integer	2023
ps_analysis_in_progress	Used within the pregnancy_helper_function to signify that analysis is currently being conducted	Boolean	False
alternative_anc_coverage	Signals within the analysis event that an alternative level of ANC coverage has been determined following the events run	Boolean	False
alternative_anc_quality	Signals within the analysis event that an alternative level of ANC quality has been determined following the events run	Boolean	False
anc_availability_odds	Target odds of early initiation of ANC4+ when analysis is being conducted - only applied ifalternative_anc_coverage is true	Real	9.0
anc_availability_probability	Target probability of quality/consumables when analysis is being conducted - only applied if alternative_anc_quality is true	Real	0.9
alternative_ip_anc_quality	Signals within the analysis event that an alternative level of inpatient ANC quality has been determined following the events run	Boolean	False
ip_anc_availability_probability	Target probability of quality/consumables when analysis is being conducted - only applied if alternative_ip_anc_quality is true	Real	0.9
sens_analysis_min	Signals within the analysis event and code that sensitivity analysis is being undertaken in which ANC is blocked from occurring	Boolean	False
sens_analysis_max	Signals within the analysis event and code that sensitivity analysis is being undertaken in which the maximum coverage of ANC is enforced	Boolean	False

ProstateCancer

Name	Description	Type	Value
init_prop_prostate_ca_stage	initial proportions in prostate cancer stages for men aged 35-49	List	[0.0001, 0.0001, 5e-05]
init_prop_urinary_symptoms_by_stage	initial proportions of those in prostate ca stages that have urinary symptoms	List	[0.3, 0.5, 0.7]
init_prop_pelvic_pain_symptoms_by_stage	initial proportions of those in prostate ca stages that have pelvic pain symptoms	List	[0.0, 0.3, 0.7]
init_prop_with_urinary_symptoms_diagnosed_prostate_ca_by_stage	initial proportions of people with prostate ca and urinary symptoms that have been diagnosed	List	[0.3, 0.4, 0.5]
init_prop_with_pelvic_pain_symptoms_diagnosed_prostate_ca_by_stage	initial proportions of people with prostate ca and pelvic pain symptoms that have been diagnosed	List	[0.3, 0.4, 0.5]
init_prop_treatment_status_prostate_ca	initial proportions of people with prostate ca that had received treatment	List	[0.1, 0.1, 0.1]
init_prob_palliative_care	initial probability of being under palliative care if at metastatic stage	Real	0.95
r_prostate_confined_prostate_ca_none	probabilty per 3 months of incident (prostate confined) prostate cancer amongst people with no prostate ca (men, age35-49)	Real	4e-05
rr_prostate_confined_prostate_ca_age5069	rate ratio for incident (prostate confined) prostate cancer amongst men aged 50-69	Real	2.0
rr_prostate_confined_prostate_ca_agege70	rate ratio for incident (prostate confined) prostate cancer amongst men aged ge 70	Real	4.0
r_local_ln_prostate_ca_prostate_confined	probabilty per 3 months of local lymph node involved prostate ca amongst people with prostate confined prostate ca	Real	0.15
rr_local_ln_prostate_ca_undergone_curative_treatment	rate ratio for local lymph node involved prostate ca for people with prostate confined prostate cadue to undergoing curative treatment	Real	0.1
r_metastatic_prostate_ca_local_ln	probabilty per 3 months of metastatic prostate cancer amongst people with local lymph nodeinvolved prostate ca	Real	0.15
rr_metastatic_prostate_ca_undergone_curative_treatment	rate ratio for metastatic prostate cancer stage 1 for people with lymph node involved prostate ca due toundergoing curative treatment	Real	0.2
r_death_metastatic_prostate_cancer	probabilty per 3 months of death from prostate cancer mongst people with metastatic prostate cancer	Real	0.2
r_urinary_symptoms_prostate_ca	rate of urinary symptoms if have prostate confined prostate ca	Real	0.05
rr_urinary_symptoms_local_ln_or_metastatic_prostate_cancer	rate ratio of urinary symptoms in a person with local lymph node or metastatuc prostate cancer compared with prostate confined prostate ca	Real	1.5
r_pelvic_pain_symptoms_local_ln_prostate_ca	rate of pelvic pain or numbness symptoms if have local lymph node involved prostate cancer	Real	0.05
rr_pelvic_pain_metastatic_prostate_cancer	rate ratio of pelvic pain or numbness in a person with metastatic prostate cancer compared with lymph node involved prostate cancer	Real	1.5
rp_prostate_cancer_age5069	stage-specific relative prevalence at baseline of prostate cancer for age 50-69	Real	2.0
rp_prostate_cancer_agege70	stage-specific relative prevalence at baseline of prostate cancer for age 70+	Real	4.0
sensitivity_of_psa_test_for_prostate_ca	sensitivity of psa test for prostate cancer	Real	0.9
sensitivity_of_biopsy_for_prostate_ca	sensitivity of biopsy for prostate cancer	Real	0.95

RTI

Name	Description	Type	Value
base_rate_injrti	Base rate of RTI per year	Real	0.00420322902234662
rr_injrti_age04	risk ratio of RTI in age 0-4 compared to base rate of RTI	Real	0.145533
rr_injrti_age59	risk ratio of RTI in age 5-9 compared to base rate of RTI	Real	0.551895
rr_injrti_age1017	risk ratio of RTI in age 10-17 compared to base rate of RTI	Real	0.967017
rr_injrti_age1829	risk ratio of RTI in age 18-29 compared to base rate of RTI	Real	1.184184
rr_injrti_age3039	risk ratio of RTI in age 30-39 compared to base rate of RTI	Real	1.052843
rr_injrti_age4049	risk ratio of RTI in age 40-49 compared to base rate of RTI	Real	1.074376
rr_injrti_age5059	risk ratio of RTI in age 50-59 compared to base rate of RTI	Real	1.336449
rr_injrti_age6069	risk ratio of RTI in age 60-69 compared to base rate of RTI	Real	2.308514
rr_injrti_age7079	risk ratio of RTI in age 70-79 compared to base rate of RTI	Real	4.031226
rr_injrti_male	risk ratio of RTI when male compared to females	Real	2.7
rr_injrti_excessalcohol	risk ratio of RTI in those that consume excess alcohol compared to those who do not	Real	6.53
imm_death_proportion_rti	Proportion of those involved in an RTI that die at site of accident or die before seeking medical intervention	Real	0.007
prob_bleeding_leads_to_shock	The proportion of those with heavily bleeding injuries who go into shock	Real	0.042222
prob_death_iss_less_than_9	Proportion of people who pass away in the following month after medical treatment for injuries with an ISSscore less than or equal to 9	Real	0.00733191462346883
prob_death_iss_10_15	Proportion of people who pass away in the following month after medical treatment for injuries with an ISSscore from 10 to 15	Real	0.0111021545889758
prob_death_iss_16_24	Proportion of people who pass away in the following month after medical treatment for injuries with an ISSscore from 16 to 24	Real	0.0313608577284893
prob_death_iss_25_35	Proportion of people who pass away in the following month after medical treatment for injuries with an ISSscore from 25 to 34	Real	0.133987145668097
prob_death_iss_35_plus	Proportion of people who pass away in the following month after medical treatment for injuries with an ISSscore 35 and above	Real	0.22782740761579
prob_perm_disability_with_treatment_severe_TBI	probability that someone with a treated severe TBI is permanently disabled	Real	0.199
prob_death_TBI_SCI_no_treatment	probability that someone with a spinal cord injury will die without treatment	Real	0.9
prop_death_burns_no_treatment	probability that someone with a burn injury will die without treatment	Real	0.6
prob_death_fractures_no_treatment	probability that someone with a fracture injury will die without treatment	Real	0.1
prob_TBI_require_craniotomy	probability that someone with a traumatic brain injury will require a craniotomy surgery	Real	0.124
prob_exploratory_laparotomy	probability that someone with an internal organ injury will require a exploratory_laparotomy	Real	0.319
prob_depressed_skull_fracture	Probability that a skull fracture will be depressed and therefore require surgery	Real	0.14
prob_mild_burns	Probability that a burn within a region will result in < 10% total body surface area	Real	0.56
prob_dislocation_requires_surgery	Probability that a dislocation will require surgery to relocate the joint.	Real	0.01
number_of_injured_body_regions_distribution	The distribution of number of injured AIS body regions, used to decide how many injuries a person has	List	[[1, 2, 3, 4, 5, 6, 7, 8], [0.7362050184224718, 0.19421990546958515, 0.051237591074077896, 0.013517104401461814, 0.0035659777825202245, 0.0009407486372638106, 0.0002481810186400668, 6.547319397917849e-05]]
injury_location_distribution	The distribution of where injuries are located in the body, based on the AIS body region definition	List	[[1, 2, 3, 4, 5, 6, 7, 8], [0.1438, 0.1325, 0.021, 0.0945, 0.0612, 0.0155, 0.1685, 0.363]]
mean_los_ISS_less_than_4	Mean length of stay for someone with an ISS score < 4	Real	4.97
sd_los_ISS_less_than_4	Standard deviation in length of stay for someone with an ISS score < 4	Real	4.86
mean_los_ISS_4_to_8	Mean length of stay for someone with an ISS score between 4 and 8	Real	8.91
sd_los_ISS_4_to_8	Standard deviation in length of stay for someone with an ISS score between 4 and 8	Real	5.93
mean_los_ISS_9_to_15	Mean length of stay for someone with an ISS score between 9 and 15	Real	15.46
sd_los_ISS_9_to_15	Standard deviation in length of stay for someone with an ISS score between 9 and 15	Real	11.16
mean_los_ISS_16_to_24	Mean length of stay for someone with an ISS score between 16 and 24	Real	24.73
sd_los_ISS_16_to_24	Standard deviation in length of stay for someone with an ISS score between 16 and 24	Real	17.03
mean_los_ISS_more_than_25	Mean length of stay for someone with an ISS score between 16 and 24	Real	30.86
sd_los_ISS_more_that_25	Standard deviation in length of stay for someone with an ISS score between 16 and 24	Real	34.03
daly_wt_unspecified_skull_fracture	daly_wt_unspecified_skull_fracture - code 1674	Real	0.195
daly_wt_basilar_skull_fracture	daly_wt_basilar_skull_fracture - code 1675	Real	0.149
daly_wt_epidural_hematoma	daly_wt_epidural_hematoma - code 1676	Real	0.185
daly_wt_subdural_hematoma	daly_wt_subdural_hematoma - code 1677	Real	0.21
daly_wt_subarachnoid_hematoma	daly_wt_subarachnoid_hematoma - code 1678	Real	0.214
daly_wt_brain_contusion	daly_wt_brain_contusion - code 1679	Real	0.174
daly_wt_intraventricular_haemorrhage	daly_wt_intraventricular_haemorrhage - code 1680	Real	0.174
daly_wt_diffuse_axonal_injury	daly_wt_diffuse_axonal_injury - code 1681	Real	0.239
daly_wt_subgaleal_hematoma	daly_wt_subgaleal_hematoma - code 1682	Real	0.174
daly_wt_midline_shift	daly_wt_midline_shift - code 1683	Real	0.239
daly_wt_facial_fracture	daly_wt_facial_fracture - code 1684	Real	0.067
daly_wt_facial_soft_tissue_injury	daly_wt_facial_soft_tissue_injury - code 1685	Real	0.008
daly_wt_eye_injury	daly_wt_eye_injury - code 1686	Real	0.054
daly_wt_neck_soft_tissue_injury	daly_wt_neck_soft_tissue_injury - code 1687	Real	0.1
daly_wt_neck_internal_bleeding	daly_wt_neck_internal_bleeding - code 1688	Real	0.1
daly_wt_neck_dislocation	daly_wt_neck_dislocation - code 1689	Real	0.187
daly_wt_chest_wall_bruises_hematoma	daly_wt_chest_wall_bruises_hematoma - code 1690	Real	0.143
daly_wt_hemothorax	daly_wt_hemothorax - code 1691	Real	0.143
daly_wt_lung_contusion	daly_wt_lung_contusion - code 1692	Real	0.205
daly_wt_diaphragm_rupture	daly_wt_diaphragm_rupture - code 1693	Real	0.205
daly_wt_rib_fracture	daly_wt_rib_fracture - code 1694	Real	0.187
daly_wt_flail_chest	daly_wt_flail_chest - code 1695	Real	0.211
daly_wt_chest_wall_laceration	daly_wt_chest_wall_laceration - code 1696	Real	0.143
daly_wt_closed_pneumothorax	daly_wt_closed_pneumothorax - code 1697	Real	0.164
daly_wt_open_pneumothorax	daly_wt_open_pneumothorax - code 1698	Real	0.164
daly_wt_surgical_emphysema	daly_wt_surgical_emphysema aka subcuteal emphysema - code 1699	Real	0.164
daly_wt_abd_internal_organ_injury	daly_wt_abd_internal_organ_injury - code 1700	Real	0.182
daly_wt_spinal_cord_lesion_neck_with_treatment	daly_wt_spinal_cord_lesion_neck_with_treatment - code 1701	Real	0.589
daly_wt_spinal_cord_lesion_neck_without_treatment	daly_wt_spinal_cord_lesion_neck_without_treatment - code 1702	Real	0.732
daly_wt_spinal_cord_lesion_below_neck_with_treatment	daly_wt_spinal_cord_lesion_below_neck_with_treatment - code 1703	Real	0.296
daly_wt_spinal_cord_lesion_below_neck_without_treatment	daly_wt_spinal_cord_lesion_below_neck_without_treatment - code 1704	Real	0.623
daly_wt_vertebrae_fracture	daly_wt_vertebrae_fracture - code 1705	Real	0.111
daly_wt_clavicle_scapula_humerus_fracture	daly_wt_clavicle_scapula_humerus_fracture - code 1706	Real	0.035
daly_wt_hand_wrist_fracture_with_treatment	daly_wt_hand_wrist_fracture_with_treatment - code 1707	Real	0.01
daly_wt_hand_wrist_fracture_without_treatment	daly_wt_hand_wrist_fracture_without_treatment - code 1708	Real	0.014
daly_wt_radius_ulna_fracture_short_term_with_without_treatment	daly_wt_radius_ulna_fracture_short_term_with_without_treatment - code 1709	Real	0.028
daly_wt_radius_ulna_fracture_long_term_without_treatment	daly_wt_radius_ulna_fracture_long_term_without_treatment - code 1710	Real	0.043
daly_wt_dislocated_shoulder	daly_wt_dislocated_shoulder - code 1711	Real	0.062
daly_wt_amputated_finger	daly_wt_amputated_finger - code 1712	Real	0.005
daly_wt_amputated_thumb	daly_wt_amputated_thumb - code 1713	Real	0.011
daly_wt_unilateral_arm_amputation_with_treatment	daly_wt_unilateral_arm_amputation_with_treatment - code 1714	Real	0.039
daly_wt_unilateral_arm_amputation_without_treatment	daly_wt_unilateral_arm_amputation_without_treatment - code 1715	Real	0.118
daly_wt_bilateral_arm_amputation_with_treatment	daly_wt_bilateral_arm_amputation_with_treatment - code 1716	Real	0.123
daly_wt_bilateral_arm_amputation_without_treatment	daly_wt_bilateral_arm_amputation_without_treatment - code 1717	Real	0.383
daly_wt_foot_fracture_short_term_with_without_treatment	daly_wt_foot_fracture_short_term_with_without_treatment - code 1718	Real	0.026
daly_wt_foot_fracture_long_term_without_treatment	daly_wt_foot_fracture_long_term_without_treatment - code 1719	Real	0.026
daly_wt_patella_tibia_fibula_fracture_with_treatment	daly_wt_patella_tibia_fibula_fracture_with_treatment - code 1720	Real	0.05
daly_wt_patella_tibia_fibula_fracture_without_treatment	daly_wt_patella_tibia_fibula_fracture_without_treatment - code 1721	Real	0.055
daly_wt_hip_fracture_short_term_with_without_treatment	daly_wt_hip_fracture_short_term_with_without_treatment - code 1722	Real	0.258
daly_wt_hip_fracture_long_term_with_treatment	daly_wt_hip_fracture_long_term_with_treatment - code 1723	Real	0.058
daly_wt_hip_fracture_long_term_without_treatment	daly_wt_hip_fracture_long_term_without_treatment - code 1724	Real	0.402
daly_wt_pelvis_fracture_short_term	daly_wt_pelvis_fracture_short_term - code 1725	Real	0.279
daly_wt_pelvis_fracture_long_term	daly_wt_pelvis_fracture_long_term - code 1726	Real	0.182
daly_wt_femur_fracture_short_term	daly_wt_femur_fracture_short_term - code 1727	Real	0.111
daly_wt_femur_fracture_long_term_without_treatment	daly_wt_femur_fracture_long_term_without_treatment - code 1728	Real	0.042
daly_wt_dislocated_hip	daly_wt_dislocated_hip - code 1729	Real	0.016
daly_wt_dislocated_knee	daly_wt_dislocated_knee - code 1730	Real	0.113
daly_wt_amputated_toes	daly_wt_amputated_toes - code 1731	Real	0.006
daly_wt_unilateral_lower_limb_amputation_with_treatment	daly_wt_unilateral_lower_limb_amputation_with_treatment - code 1732	Real	0.039
daly_wt_unilateral_lower_limb_amputation_without_treatment	daly_wt_unilateral_lower_limb_amputation_without_treatment - code 1733	Real	0.173
daly_wt_bilateral_lower_limb_amputation_with_treatment	daly_wt_bilateral_lower_limb_amputation_with_treatment - code 1734	Real	0.088
daly_wt_bilateral_lower_limb_amputation_without_treatment	daly_wt_bilateral_lower_limb_amputation_without_treatment - code 1735	Real	0.443
rt_emergency_care_ISS_score_cut_off	A parameter to determine which level of injury severity corresponds to the emergency health care seeking symptom and which to the non-emergency generic injury symptom	Integer	5
prob_death_MAIS3	A parameter to determine the probability of death without medical intervention with a military AISscore of 3	Real	0.05
prob_death_MAIS4	A parameter to determine the probability of death without medical intervention with a military AISscore of 4	Real	0.31
prob_death_MAIS5	A parameter to determine the probability of death without medical intervention with a military AISscore of 5	Real	0.59
prob_death_MAIS6	A parameter to determine the probability of death without medical intervention with a military AISscore of 6	Real	0.83
femur_fracture_skeletal_traction_mean_los	The mean length of stay for a person with a femur fracture being treated with skeletal traction	Integer	52
other_skeletal_traction_los	The mean length of stay for a person with a non-femur fracture being treated with skeletal traction	Integer	42
prob_foot_frac_require_cast	The probability that a person with a foot fracture will be treated with a plaster cast	Real	0.613
prob_foot_frac_require_maj_surg	The probability that a person with a foot fracture will be treated with a major surgery	Real	0.263
prob_foot_frac_require_min_surg	The probability that a person with a foot fracture will be treated with a major surgery	Real	0.038
prob_foot_frac_require_amp	The probability that a person with a foot fracture will be treated with amputation via a major surgery	Real	0.086
prob_tib_fib_frac_require_cast	The probability that a person with a tibia/fibula fracture will be treated with a plaster cast	Real	0.71
prob_tib_fib_frac_require_maj_surg	The probability that a person with a tibia/fibula fracture will be treated with a major surgery	Real	0.066
prob_tib_fib_frac_require_min_surg	The probability that a person with a tibia/fibula fracture will be treated with a minor surgery	Real	0.175
prob_tib_fib_frac_require_amp	The probability that a person with a tibia/fibula fracture will be treated with an amputation via major surgery	Real	0.024
prob_tib_fib_frac_require_traction	The probability that a person with a tibia/fibula fracture will be treated with skeletal traction	Real	0.025
prob_femural_fracture_require_major_surgery	The probability that a person with a femur fracture will be treated with major surgery	Real	0.187
prob_femural_fracture_require_minor_surgery	The probability that a person with a femur fracture will be treated with minor surgery	Real	0.007
prob_femural_fracture_require_cast	The probability that a person with a femur fracture will be treated with a plaster cast	Real	0.024
prob_femural_fracture_require_amputation	The probability that a person with a femur fracture will be treated with amputation via major surgery	Real	0.005
prob_femural_fracture_require_traction	The probability that a person with a femur fracture will be treated with skeletal traction	Real	0.777
prob_pelvis_fracture_traction	The probability that a person with a pelvis fracture will be treated with skeletal traction	Real	0.71
prob_pelvis_frac_major_surgery	The probability that a person with a pelvis fracture will be treated with major surgery	Real	0.12
prob_pelvis_frac_minor_surgery	The probability that a person with a pelvis fracture will be treated with minor surgery	Real	0.05
prob_pelvis_frac_cast	The probability that a person with a pelvis fracture will be treated with a cast	Real	0.12
prob_dis_hip_require_maj_surg	The probability that a person with a dislocated hip will be treated with a major surgery	Real	0.167
prob_dis_hip_require_cast	The probability that a person with a dislocated hip will be treated with a plaster cast	Real	0.333
prob_hip_dis_require_traction	The probability that a person with a dislocated hip will be treated with skeletal traction	Real	0.5
hdu_cut_off_iss_score	The ISS score used as a criteria to admit patients to the HDU/ICU units	Integer	29
mean_icu_days	The mean length of stay in the ICUfor those without TBI	Real	4.8
sd_icu_days	The standard deviation in length of stay in the ICU for those without TBI	Real	6.0
mean_tbi_icu_days	The mean length of stay in the ICU for those with TBI	Real	8.4
sd_tbi_icu_days	The standard deviation in length of stay in the ICU for those with TBI	Real	6.4
prob_open_fracture_contaminated	The probability that an open fracture will be contaminated	Real	0.07
allowed_interventions	List of additional interventions that can be included when performing model analysis	List	[]
head_prob_112	The probability that this person’s head injury is a skull fracture	Real	0.0455
head_prob_113	The probability that this person’s head injury is a basilar skull fracture	Real	0.0045
head_prob_133a	The probability that this person’s head injury is a Subarachnoid hematoma	Real	0.09149906
head_prob_133b	The probability that this person’s head injury is a Brain contusion	Real	0.301946898
head_prob_133c	The probability that this person’s head injury is an Intraventricular haemorrhage	Real	0.013724859
head_prob_133d	The probability that this person’s head injury is a Subgaleal hematoma	Real	0.050324483
head_prob_134a	The probability that this person’s head injury is an Epidural hematoma	Real	0.086670324
head_prob_134b	The probability that this person’s head injury is a Subdural hematoma	Real	0.080003376
head_prob_135	The probability that this person’s head injury is a Diffuse axonal injury/midline shift	Real	0.061731
head_prob_1101	The probability that this person’s head injury is a laceration	Real	0.253536
head_prob_1114	The probability that this person’s head injury is a burn	Real	0.010564
face_prob_211	The probability that this person’s face injury is a Facial fracture (nasal/unspecified)	Real	0.158585
face_prob_212	The probability that this person’s face injury is a Facial fracture (mandible/zygomatic)	Real	0.294515
face_prob_241	The probability that this person’s face injury is a soft tissue injury	Real	0.339
face_prob_2101	The probability that this person’s face injury is a laceration	Real	0.194845
face_prob_2114	The probability that this person’s face injury is a burn	Real	0.010255
face_prob_291	The probability that this person’s face injury is an eye injury	Real	0.0028
neck_prob_3101	The probability that this person’s neck injury is a laceration	Real	0.06972
neck_prob_3113	The probability that this person’s neck injury is a burn	Real	0.01428
neck_prob_342	The probability that this person’s neck injury is a Soft tissue injury in neck (vertebral artery laceration)	Real	0.004
neck_prob_343	The probability that this person’s neck injury is a Soft tissue injury in neck (pharynx contusion)	Real	0.004
neck_prob_361	The probability that this person’s neck injury is a Sternomastoid m. hemorrhage/ Hemorrhage, supraclavicular triangle/Hemorrhage, posterior triangle/Anterior vertebral vessel hemorrhage/ Neck muscle hemorrhage	Real	0.495
neck_prob_363	The probability that this person’s neck injury is a Hematoma in carotid sheath/Carotid sheath hemorrhage	Real	0.405
neck_prob_322	The probability that this person’s neck injury is an Atlanto-occipital subluxation	Real	0.00264
neck_prob_323	The probability that this person’s neck injury is an Atlanto-axial subluxation	Real	0.00536
thorax_prob_4101	The probability that this person’s thorax injury is a laceration	Real	0.49036
thorax_prob_4113	The probability that this person’s thorax injury is a burn	Real	0.04264
thorax_prob_461	The probability that this person’s thorax injury is Chest wall bruises/haematoma	Real	0.0945
thorax_prob_463	The probability that this person’s thorax injury is Haemothorax	Real	0.0945
thorax_prob_453a	The probability that this person’s thorax injury is a Lung contusion	Real	0.0539
thorax_prob_453b	The probability that this person’s thorax injury is a Diaphragm rupture	Real	0.0161
thorax_prob_412	The probability that this person’s thorax injury is a rib fracture	Real	0.0392
thorax_prob_414	The probability that this person’s thorax injury is flail chest	Real	0.0098
thorax_prob_441	The probability that this person’s thorax injury is a Chest wall lacerations/avulsions	Real	0.08586
thorax_prob_442	The probability that this person’s thorax injury is a Surgical emphysema	Real	0.01749
thorax_prob_443	The probability that this person’s thorax injury is a Closed pneumothorax/ open pneumothorax	Real	0.05565
abdomen_prob_5101	The probability that this person’s abdomen injury is a laceration	Real	0.11026
abdomen_prob_5113	The probability that this person’s thorax injury is a burn	Real	0.03874
abdomen_prob_552	The probability that this person’s thorax injury is a skull fracture	Real	0.047656
abdomen_prob_553	The probability that this person’s thorax injury is an Injury to stomach/intestines/colon	Real	0.77441
abdomen_prob_554	The probability that this person’s thorax injury is an Injury to spleen/Urinary bladder/Liver/Urethra/Diaphragm	Real	0.028934
spine_prob_612	The probability that this person’s spine injury is a vertabrae fracture	Real	0.364
spine_prob_673a	The probability that this person’s spine injury is a Spinal cord injury at neck level	Real	0.015840216
spine_prob_673b	The probability that this person’s spine injury is a Spinal cord injury below neck level	Real	0.040731984
spine_prob_674a	The probability that this person’s spine injury is a Spinal cord injury at neck level	Real	0.074477731
spine_prob_674b	The probability that this person’s spine injury is a Spinal cord injury below neck level	Real	0.116490809
spine_prob_675a	The probability that this person’s spine injury is a Spinal cord injury at neck level	Real	0.134791137
spine_prob_675b	The probability that this person’s spine injury is a Spinal cord injury below neck level	Real	0.210827163
spine_prob_676	The probability that this person’s spine injury is a Spinal cord injury at neck level	Real	0.04284096
upper_ex_prob_7101	The probability that this person’s upper extremity injury is a laceration	Real	0.43896
upper_ex_prob_7113	The probability that this person’s upper extremity injury is a burn	Real	0.03304
upper_ex_prob_712a	The probability that this person’s upper extremity injury is a Fracture to Clavicle, scapula, humerus	Real	0.10802
upper_ex_prob_712b	The probability that this person’s upper extremity injury is a Fracture to Hand/wrist	Real	0.28969
upper_ex_prob_712c	The probability that this person’s upper extremity injury is a Fracture to Radius/ulna	Real	0.09329
upper_ex_prob_722	The probability that this person’s upper extremity injury is a dislocated shoulder	Real	0.025
upper_ex_prob_782a	The probability that this person’s upper extremity injury is an Amputated finger	Real	0.00750024
upper_ex_prob_782b	The probability that this person’s upper extremity injury is a Unilateral arm amputation	Real	0.00102276
upper_ex_prob_782c	The probability that this person’s upper extremity injury is a Thumb amputation	Real	0.002841
upper_ex_prob_783	The probability that this person’s upper extremity injury is a bilateral arm amputation	Real	0.000636
lower_ex_prob_8101	The probability that this person’s lower extremity injury is a laceration	Real	0.186094109
lower_ex_prob_8113	The probability that this person’s lower extremity injury is a burn	Real	0.014007083
lower_ex_prob_811	The probability that this person’s lower extremity injury is a foot fracture	Real	0.023610948
lower_ex_prob_813do	The probability that this person’s lower extremity injury is an open foot fracture	Real	0.013281158
lower_ex_prob_812	The probability that this person’s lower extremity injury is a Fracture to patella, tibia, fibula, ankle	Real	0.354164215
lower_ex_prob_813eo	The probability that this person’s lower extremity injury is an open Fracture to patella, tibia, fibula, ankle	Real	0.199217371
lower_ex_prob_813a	The probability that this person’s lower extremity injury is a Hip fracture	Real	0.029513685
lower_ex_prob_813b	The probability that this person’s lower extremity injury is a Pelvis fracture	Real	0.023610948
lower_ex_prob_813bo	The probability that this person’s lower extremity injury is an open Pelvis fracture	Real	0.005902737
lower_ex_prob_813c	The probability that this person’s lower extremity injury is a Femur fracture	Real	0.076765094
lower_ex_prob_813co	The probability that this person’s lower extremity injury is an open Femur fracture	Real	0.01177596
lower_ex_prob_822a	The probability that this person’s lower extremity injury is a Dislocated hip	Real	0.037338982
lower_ex_prob_822b	The probability that this person’s lower extremity injury is a Dislocated knee	Real	0.002383339
lower_ex_prob_882	The probability that this person’s lower extremity injury is an Amputation of toes	Real	0.00731139
lower_ex_prob_883	The probability that this person’s lower extremity injury is a Unilateral leg amputation	Real	0.007511491
lower_ex_prob_884	The probability that this person’s lower extremity injury is a Bilateral leg amputation	Real	0.007511491
blocked_interventions	A list of interventions that are blocked in a simulation	List	[]
unavailable_treatment_mortality_mais_cutoff	A cut-off score above which an injury will result in additional mortality if the person has sought healthcare and not received it.	Integer	5
consider_death_no_treatment_ISS_cut_off	A cut-off score above which an injuries will be considered severe enough to cause mortality in those whohave not sought care.	Integer	15
maximum_number_of_times_HSI_events_should_run	limit on the number of times an HSI event can run	Integer	5

Schisto

Name	Description	Type	Value
prob_sent_to_lab_test_children	Probability that infected child gets sent to lab test	Real	0.9
prob_sent_to_lab_test_adults	Probability that an infected adults gets sent to lab test	Real	0.6
delay_till_hsi_a_repeated	Time till seeking healthcare again after not being sent to schisto test: start	Real	5.0
delay_till_hsi_b_repeated	Time till seeking healthcare again after not being sent to schisto test: end	Real	20.0
PZQ_efficacy	The efficacy of Praziquantel in clearing burden of any Schistosomiasis worm species	Real	1.0
MDA_coverage_historical	Probability of getting PZQ in the MDA for PSAC, SAC and Adults in historic rounds	Dataframe	…
MDA_coverage_prognosed	Probability of getting PZQ in the MDA for PSAC, SAC and Adults in future rounds, with the frequency given in months	Dataframe	…
sm_beta_PSAC	Contact/exposure rate of PSAC	Real	0.3
sm_beta_SAC	Contact/exposure rate of SAC	Real	1.0
sm_beta_Adults	Contact/exposure rate of Adults	Real	0.05
sm_worms_fecundity	Fecundity parameter, driving density-dependent reproduction	Real	0.0006
sm_worm_lifespan	Lifespan of the worm in human host given in years	Real	4.0
sm_high_intensity_threshold	Threshold of worm burden indicating high intensity infection	Real	46.0
sm_low_intensity_threshold	Threshold of worm burden indicating low intensity infection	Real	2.0
sm_high_intensity_threshold_PSAC	Worm burden threshold for high intensity infection in PSAC	Real	20.0
sm_reservoir_2010	Initial reservoir of infectious material per district in 2010	Series	…
sm_gamma_alpha	Parameter alpha for Gamma distribution for harbouring rates	Series	…
sm_R0	Effective reproduction number, for the FOI	Series	…
sh_beta_PSAC	Contact/exposure rate of PSAC	Real	0.3
sh_beta_SAC	Contact/exposure rate of SAC	Real	1.0
sh_beta_Adults	Contact/exposure rate of Adults	Real	0.05
sh_worms_fecundity	Fecundity parameter, driving density-dependent reproduction	Real	0.005
sh_worm_lifespan	Lifespan of the worm in human host given in years	Real	6.0
sh_high_intensity_threshold	Threshold of worm burden indicating high intensity infection	Real	20.0
sh_low_intensity_threshold	Threshold of worm burden indicating low intensity infection	Real	2.0
sh_high_intensity_threshold_PSAC	Worm burden threshold for high intensity infection in PSAC	Real	5.0
sh_reservoir_2010	Initial reservoir of infectious material per district in 2010	Series	…
sh_gamma_alpha	Parameter alpha for Gamma distribution for harbouring rates	Series	…
sh_R0	Effective reproduction number, for the FOI	Series	…

MDA_coverage_historical

PSAC	SAC	Adults
0	0.85	0.44
0	0.92	0.88
0	0.87	0.88
0	0.73	0.02
0	0.8	0.155
0	0.87	0.29
0	0.87	0.9
0	0.48	0.96
0	0.605	0.96

Only first 10 rows of 128 are shown.

MDA_coverage_prognosed

PSAC	SAC	Adults
0.5	0.8	0.5
0.5	0.8	0.5
0.5	0.8	0.5
0.5	0.8	0.5
0.5	0.8	0.5
0	0.8	0.5
0	0.8	0.5
0	0.8	0.5
0	0.8	0.5

Only first 10 rows of 32 are shown.

sm_reservoir_2010

Reservoir
0.0796066
0.0796066
0.0243277
0.158777
0
0
0
0.0891927
0

Only first 10 rows of 32 are shown.

sm_gamma_alpha

alpha_value
0.0652093
0.0652093
0.056
0.07445
0.05
0.05
0.05
0.0665
0.05

Only first 10 rows of 32 are shown.

sm_R0

R0_value
1.46175
1.46175
2.18968
1.26817
0
0
0
1.42196
0

Only first 10 rows of 32 are shown.

sh_reservoir_2010

Reservoir
1.87216
0
0
2.81222
0
0
0
0
0

Only first 10 rows of 32 are shown.

sh_gamma_alpha

alpha_value
0.107616
0.04664
0.0805
0.1377
0.08905
0.0698
0
0.0643
0.0793714

Only first 10 rows of 32 are shown.

sh_R0

R0_value
1.12956
1.1253
1.1248
1.14141
1.12577
1.12423
0
1.12421
1.12471

Only first 10 rows of 32 are shown.

Stunting

Name	Description	Type	Value
prev_HAZ_distribution_age_0_5mo	Distribution of HAZ among less than 6 months of age in 2015 (mean, standard deviation)	List	[-0.8482365, 1.416337]
prev_HAZ_distribution_age_6_11mo	Distribution of HAZ among 6 months and 1 year of age in 2015 (mean, standard deviation)	List	[-0.9940219, 1.504431]
prev_HAZ_distribution_age_12_23mo	Distribution of HAZ among 1 year olds in 2015 (mean, standard deviation)	List	[-1.522101, 1.431207]
prev_HAZ_distribution_age_24_35mo	Distribution of HAZ among 2 year olds in 2015 (mean, standard deviation)	List	[-1.669291, 1.343577]
prev_HAZ_distribution_age_36_47mo	Distribution of HAZ among 3 year olds in 2015 (mean, standard deviation)	List	[-1.797365, 1.212469]
prev_HAZ_distribution_age_48_59mo	Distribution of HAZ among 4 year olds in 2015 (mean, standard deviation)	List	[-1.620094, 1.11541]
or_stunting_male	Odds ratio of stunting if male gender	Real	1.38
or_stunting_preterm_and_AGA	Odds ratio of stunting if born preterm and adequate for gestational age	Real	2.13
or_stunting_SGA_and_term	Odds ratio of stunting if born term and small for geatational age	Real	2.36
or_stunting_SGA_and_preterm	Odds ratio of stunting if born preterm and small for gestational age	Real	5.95
or_stunting_hhwealth_Q5	Odds ratio of stunting if household wealth is poorest Q5, ref group Q1	Real	1.69
or_stunting_hhwealth_Q4	Odds ratio of stunting if household wealth is poorer Q4, ref group Q1	Real	1.48
or_stunting_hhwealth_Q3	Odds ratio of stunting if household wealth is middle Q3, ref group Q1	Real	1.4
or_stunting_hhwealth_Q2	Odds ratio of stunting if household wealth is richer Q2, ref group Q1	Real	1.29
base_inc_rate_stunting_by_agegp	Baseline incidence rate per year of stunting by age group (1-5, 6-11, 12-23, 24-35, 36-47, 48-59mo	List	[0.8, 0.8, 0.8, 0.8, 0.8, 0.8]
rr_stunting_preterm_and_AGA	Relative risk of stunting if born preterm and adequate for gestational age	Real	1.62
rr_stunting_SGA_and_term	Relative risk of stunting if born term and small for gestational age	Real	1.65
rr_stunting_SGA_and_preterm	Relative risk of stunting if born preterm and small for gestational age	Real	2.98
rr_stunting_prior_wasting	Relative risk of stunting if prior wasting in the last 3 months	Real	1.93
rr_stunting_untreated_HIV	Relative risk of stunting for untreated HIV+	Real	1.5
rr_stunting_wealth_level	Relative risk of stunting if wealth-level is greater than 1 compared 1	Real	0.2
rr_stunting_no_exclusive_breastfeeding	Relative risk of stunting for not exclusively breastfed babies < 6 months	Real	1.4
rr_stunting_no_continued_breastfeeding	Relative risk of stunting for not continued breastfed infants 6-24 months	Real	1.3
rr_stunting_per_diarrhoeal_episode	Relative risk of stunting for recent diarrhoea episode	Real	1.04
r_progression_severe_stunting_by_agegp	Rates per year of progression to severe stunting by age group (1-5, 6-11, 12-23, 24-35, 36-47, 48-59mo	List	[0.8, 0.8, 0.8, 0.8, 0.8, 0.8]
rr_progress_severe_stunting_if_prior_wasting	Relative risk of severe stunting if previously wasted	Real	1.93
rr_progress_severe_stunting_untreated_HIV	Relative risk of severe stunting for untreated HIV+	Real	1.3
mean_years_to_1stdev_natural_improvement_in_stunting	Mean time (in years) to a one standard deviation improvement in stunting without any treatment.	Real	1.840675229013975
effectiveness_of_complementary_feeding_education_in_stunting_reduction	Probability of stunting being reduced by one standard deviation (category) by education about supplementary feeding (but not supplying supplementary feeding consmables).	Real	0.25
effectiveness_of_food_supplementation_in_stunting_reduction	Probability of stunting being reduced by one standard deviation (category) by supplementary feeding.	Real	0.41
prob_stunting_diagnosed_at_generic_appt	Probability of a stunted or severely stunted person being checked and correctly diagnosed	Real	0.01

SymptomManager

Name	Description	Type	Value
generic_symptoms_spurious_occurrence	probability and duration of spurious occureneces of generic symptoms	Dataframe	…
spurious_symptoms	whether or not there will be the spontaneous occurrence of generic symptoms. NB. This is over-ridden if a module key-word argument is provided.	Boolean	True

generic_symptoms_spurious_occurrence

name	odds_ratio_health_seeking_in_children	odds_ratio_health_seeking_in_adults	prob_spurious_occurrence_in_children_per_day	prob_spurious_occurrence_in_adults_per_day	duration_in_days_of_spurious_occurrence_in_children	duration_in_days_of_spurious_occurrence_in_adults	prob_seeks_emergency_appt_in_adults	prob_seeks_emergency_appt_in_children
vomiting	1.31	0.48	0.001	0.001	7	4	0	0
stomachache	0.7	0.48	0.001	0.001	7	4	0	0
sore_throat	1.07	0.58	0.001	0.001	7	4	0	0
respiratory_symptoms	0.55	0.48	0.001	0.001	7	4	0	0
headache	0.39	0.28	0.001	0.001	7	4	0	0
skin_complaint	2.82	0.76	0.001	0.001	7	4	0	0
dental_complaint	0.39	0.92	0.001	0.001	7	4	0	0
backache	1	0.56	0.001	0.001	7	4	0	0
injury	0.55	0.68	0.001	0.001	7	4	0	0

Only first 10 rows of 13 are shown.

Tb

Name	Description	Type	Value
prop_mdr2010	Proportion of active tb cases with multidrug resistance in 2010	Real	0.0186
followup_times	times(weeks) tb treatment monitoring required after tx start	Dataframe	…
tb_high_risk_distr	list of ten high-risk districts	Dataframe	…
ipt_coverage	national estimates of coverage of IPT in PLHIV and paediatric contacts	Dataframe	…
rr_tb_child	relative risk of tb infection if under 16 years of age	Real	0.1
monthly_prob_relapse_tx_complete	monthly probability of relapse once treatment complete	Real	0.0027
monthly_prob_relapse_tx_incomplete	monthly probability of relapse if treatment incomplete	Real	0.0116
monthly_prob_relapse_2yrs	monthly probability of relapse 2 years after treatment complete	Real	0.0001
rr_relapse_hiv	relative risk of relapse for HIV-positive people	Real	4.7
rr_relapse_diabetes	relative risk of relapse for people with diabetes (treated/untreated)	Real	1.86
scaling_factor_WHO	scaling factor applied to WHO estimates to account for the impact of interventions in place	Real	1.60303
duration_active_disease_years	duration of active disease from onset to cure or death	Real	3.0
prop_smear_positive	proportion of new active cases that will be smear-positive	Real	0.62
prop_smear_positive_hiv	proportion of hiv+ active tb cases that will be smear-positive	Real	0.35
death_rate_smear_pos_untreated	probability of death in smear-positive tb cases with untreated tb	Real	0.7
death_rate_smear_neg_untreated	probability of death in smear-negative tb cases with untreated tb	Real	0.2
death_rate_child0_4_treated	probability of death in child aged 0-4 years with treated tb	Real	0.05
death_rate_child5_14_treated	probability of death in child aged 5-14 years with treated tb	Real	0.06
death_rate_adult_treated	probability of death in adult aged >=15 years with treated tb	Real	0.107
rr_death_diabetes	additional risk of death if person has diabetes (treated/untreated)	Real	1.51
rr_tb_bcg	relative risk of progression to active disease for children with BCG vaccine	Real	0.42
rr_tb_hiv	relative risk of progression to active disease for PLHIV	Real	5.0
rr_tb_aids	relative risk of progression to active disease for PLHIV with AIDS	Real	26.0
rr_tb_art_adult	relative risk of progression to active disease for adults with HIV on ART	Real	0.35
rr_tb_art_child	relative risk of progression to active disease for adults with HIV on ART	Real	0.3
rr_tb_obese	relative risk of progression to active disease if obese	Real	0.4
rr_tb_diabetes	relative risk of progression to active disease with any type diabetes	Real	3.0
rr_tb_alcohol	relative risk of progression to active disease with heavy alcohol use	Real	2.9
rr_tb_smoking	relative risk of progression to active disease with smoking	Real	1.3
rr_ipt_adult	relative risk of active TB with IPT in adults	Real	0.4
rr_ipt_child	relative risk of active TB with IPT in children	Real	0.55
rr_ipt_adult_hiv	relative risk of active TB with IPT in adults with hiv	Real	0.68
rr_ipt_child_hiv	relative risk of active TB with IPT in children with hiv	Real	0.31
rr_ipt_art_adult	relative risk of active TB with IPT and ART in adults	Real	0.63
rr_ipt_art_child	relative risk of active TB with IPT and ART in children	Real	0.76
sens_xpert_smear_negative	sensitivity of Xpert test in smear negative TB cases	Real	0.68
sens_xpert_smear_positive	sensitivity of Xpert test in smear positive TB cases	Real	0.98
spec_xpert_smear_negative	specificity of Xpert test in smear negative TB cases	Real	0.99
spec_xpert_smear_positive	specificity of Xpert test in smear positive TB cases	Real	0.99
sens_sputum_smear_positive	sensitivity of sputum smear microscopy in sputum positive cases	Real	1.0
spec_sputum_smear_positive	specificity of sputum smear microscopy in sputum positive cases	Real	1.0
sens_clinical	sensitivity of clinical diagnosis in detecting active TB	Real	0.209
spec_clinical	specificity of clinical diagnosis in detecting TB	Real	0.953
sens_xray_smear_negative	sensitivity of x-ray diagnosis in smear negative TB cases	Real	0.8
sens_xray_smear_positive	sensitivity of x-ray diagnosis in smear positive TB cases	Real	0.91
spec_xray_smear_negative	specificity of x-ray diagnosis in smear negative TB cases	Real	0.67
spec_xray_smear_positive	specificity of x-ray diagnosis in smear positive TB cases	Real	0.67
prob_tx_success_ds	Probability of treatment success for new and relapse TB cases	Real	0.837
prob_tx_success_mdr	Probability of treatment success for MDR-TB cases	Real	0.597
prob_tx_success_0_4	Probability of treatment success for children aged 0-4 years	Real	0.94
prob_tx_success_5_14	Probability of treatment success for children aged 5-14 years	Real	0.92
rate_testing_general_pop	rate of screening / testing per month in general population	Real	0.025
rate_testing_active_tb	rate of screening / testing per month in population with active tb	Dataframe	…
ds_treatment_length	length of treatment for drug-susceptible tb (first case) in months	Real	6.0
ds_retreatment_length	length of treatment for drug-susceptible tb (secondary case) in months	Real	8.0
mdr_treatment_length	length of treatment for mdr-tb in months	Real	24.0
prob_retained_ipt_6_months	probability of being retained on IPT every 6 months if still eligible	Real	0.9
age_eligibility_for_ipt	eligibility criteria (years of age) for IPT given to contacts of TB cases	Real	5.0
ipt_start_date	year from which IPT is available for paediatric contacts of diagnosed active TB cases	Integer	2014
first_line_test	name of first test to be used for TB diagnosis	String	sputum
second_line_test	name of second test to be used for TB diagnosis	String	xpert
tb_healthseekingbehaviour_cap	number of repeat visits assumed for healthcare services	Integer	5
data_end	last year for which data are available	Integer	2022
length_of_inpatient_stay_if_terminal	length of inpatient stay for end-of-life TB patients	List	[5, 10]
type_of_scaleup	argument to determine type scale-up of program which will be implemented, can be ‘none’, ‘target’ or ‘max’	String	none
scaleup_start_year	the year when the scale-up starts (it will occur on 1st January of that year)	Integer	2025
scaleup_parameters	the parameters and values changed in scenario analysis	Dataframe	…

followup_times

ds_sputum	ds_clinical_monitor	ds_retreatment_sputum	ds_retreatment_clinical	mdr_sputum	mdr_clinical_monitor	shine_sputum	shine_clinical_monitor
5	2	5	2	5	2	4	2
6	3	8	3	6	3	nan	3
nan	4	nan	4	8	4	nan	4
nan	5	nan	5	10	5	nan	nan
nan	6	nan	6	12	6	nan	nan
nan	nan	nan	7	14	7	nan	nan
nan	nan	nan	8	16	8	nan	nan
nan	nan	nan	nan	18	9	nan	nan
nan	nan	nan	nan	20	10	nan	nan

Only first 10 rows of 24 are shown.

tb_high_risk_distr

district_name
Blantyre
Blantyre City
Chikwawa
Chiradzulu
Chitipa
Dedza
Dowa
Karonga
Kasungu

Only first 10 rows of 32 are shown.

ipt_coverage

year	coverage_plhiv	source	coverage_paediatric	source2
2011	0	not_implemented	0	nan
2012	0	not_implemented	0	nan
2013	0	not_implemented	0	nan
2014	0	not_implemented	35	NTP2019
2015	0	not_implemented	42	NTP2019
2016	0	not_implemented	51	NTP2019
2017	0	not_implemented	61	NTP2019
2018	0.31	MoH_quart_repQ1	57	NTP2019
2019	0.3	MoH_quart_repQ2	57	NTP2020

Only first 10 rows of 41 are shown.

rate_testing_active_tb

year	case_notification_rate_per_100k	treatment_coverage	treatment_success_rates	death_rate	percent_hiv_positive	number_notified_mdr_cases	percent_mdr_treatment_success	percent_death_mdr_cases	coverage_ipt_paediatric_contacts
2011	nan	46	82.7	10.7	nan	nan	nan	nan	nan
2012	138	51	81.8	10.7	nan	27	63.2	31.6	nan
2013	126	48	83.3	9.8	nan	91	52.6	36.8	nan
2014	112	46	85	8.9	nan	106	58.6	34	35
2015	105	46	81.6	10.6	42.6	107	60.9	32.8	42
2016	101	47	82.1	10.3	38.8	66	58.6	29.3	51
2017	95	50	86	9.7	39.1	85	55	35	61
2018	88	48	87.2	8.6	38.5	126	68.8	17	57
2019	92	51	87.6	8.2	35.5	104	73	16	57

Only first 10 rows of 12 are shown.

scaleup_parameters

parameter	target_value	min_value	max_value
tb_treatment_coverage	90	0	100
tb_prob_tx_success_ds	0.9	0	1
tb_prob_tx_success_mdr	0.9	0	1
tb_prob_tx_success_0_4	0.9	0	1
tb_prob_tx_success_5_14	0.9	0	1
first_line_test	xpert	sputum	xpert
second_line_test	sputum	sputum	xpert
ipt_coverage_plhiv	0.9	0	1
ipt_coverage_paediatric	90	0	100